Biomarkers and methods for determining sensitivity to microtubule-stabilizing agents

ABSTRACT

Biomarkers that are useful for identifying a mammal that will respond therapeutically or is responding therapeutically to a method of treating cancer that comprises administering a microtubule-stabilizing agent. In one aspect, the cancer is breast cancer, and the microtubule-stabilizing agent is an epothilone or analog or derivative thereof, or ixabepilone.

This application claims the benefit of U.S. Provisional Application No.60/631,993 filed Nov. 30, 2004, and is a continuation of U.S.Non-Provisional application Ser. No. 11/289,102 filed Nov. 29, 2005,whose contents are hereby incorporated by reference in its entirety.

SEQUENCE LISTING

A compact disc labeled “Copy 1” contains the Sequence Listing as 10338NP.ST25.txt. The Sequence Listing is 1686 KB in size and was recordedNov. 29, 2005. The compact disk is 1 of 2 compact disks. A duplicatecopy of the compact disc is labeled “Copy 2” and is 2 of 2 compactdiscs.

The compact disc and duplicate copy are identical and are herebyincorporated by reference into the present application.

FIELD OF THE INVENTION

The present invention relates generally to the field ofpharmacogenomics, and more specifically to methods and procedures todetermine drug sensitivity in patients to allow the identification ofindividualized genetic profiles which will aid in treating diseases anddisorders.

BACKGROUND OF THE INVENTION

Cancer is a disease with extensive histoclinical heterogeneity. Althoughconventional histological and clinical features have been correlated toprognosis, the same apparent prognostic type of tumors varies widely inits responsiveness to therapy and consequent survival of the patient.

New prognostic and predictive markers, which would facilitate anindividualization of therapy for each patient, are needed to accuratelypredict patient response to treatments, such as small molecule orbiological molecule drugs, in the clinic. The problem may be solved bythe identification of new parameters that could better predict thepatient's sensitivity to treatment. The classification of patientsamples is a crucial aspect of cancer diagnosis and treatment. Theassociation of a patient's response to a treatment with molecular andgenetic markers can open up new opportunities for treatment developmentin non-responding patients, or distinguish a treatment's indicationamong other treatment choices because of higher confidence in theefficacy. Further, the pre-selection of patients who are likely torespond well to a medicine, drug, or combination therapy may reduce thenumber of patients needed in a clinical study or accelerate the timeneeded to complete a clinical development program (M. Cockett et al.,Current Opinion in Biotechnology, 11:602-609 (2000)).

The ability to predict drug sensitivity in patients is particularlychallenging because drug responses reflect not only properties intrinsicto the target cells, but also a host's metabolic properties. Efforts touse genetic information to predict drug sensitivity have primarilyfocused on individual genes that have broad effects, such as themultidrug resistance genes, mdr1 and mrp1 (P. Sonneveld, J. Intern.Med., 247:521-534 (2000)).

The development of microarray technologies for large scalecharacterization of gene mRNA expression pattern has made it possible tosystematically search for molecular markers and to categorize cancersinto distinct subgroups not evident by traditional histopathologicalmethods (J. Khan et al., Cancer Res., 58:5009-5013 (1998); A. A.Alizadeh et al., Nature, 403:503-511 (2000); M. Bittner et al., Nature,406:536-540 (2000); J. Khan et al., Nature Medicine, 7(6):673-679(2001); T. R. Golub et al., Science, 286:531-537 (1999); U. Alon et al.,P. N. A. S. USA, 96:6745-6750 (1999)). Such technologies and moleculartools have made it possible to monitor the expression level of a largenumber of transcripts within a cell population at any given time (see,e.g., Schena et al., Science, 270:467-470 (1995); Lockhart et al.,Nature Biotechnology, 14:1675-1680 (1996); Blanchard et al., NatureBiotechnology, 14:1649 (1996); U.S. Pat. No. 5,569,588 to Ashby et al.).

Recent studies demonstrate that gene expression information generated bymicroarray analysis of human tumors can predict clinical outcome (L. J.van't Veer et al., Nature, 415:530-536 (2002); T. Sorlie et al., P. N.A. S. USA, 98:10869-10874 (2001); M. Shipp et al., Nature Medicine,8(1):68-74 (2002); G. Glinsky et al., The Journal of Clin. Invest.,113(6):913-923 (2004)). These findings bring hope that cancer treatmentwill be vastly improved by better predicting the response of individualtumors to therapy.

Needed are new and alternative methods and procedures to determine drugsensitivity in patients to allow the development of individualizedgenetic profiles which are necessary to treat diseases and disordersbased on patient response at a molecular level.

SUMMARY OF THE INVENTION

The invention provides methods and procedures for determining patientsensitivity to one or more microtubule-stabilizing agents. The inventionalso provides methods of determining or predicting whether an individualrequiring therapy for a disease state such as cancer will or will notrespond to treatment, prior to administration of the treatment, whereinthe treatment comprises administration of one or moremicrotubule-stabilizing agents.

In one aspect, the invention provides a method for identifying a mammalthat will respond therapeutically to a method of treating cancercomprising administering a microtubule-stabilizing agent, wherein themethod comprises: (a) measuring in the mammal the level of at least onebiomarker selected from the biomarkers of Table 1 and Table 2; (b)exposing a biological sample from the mammal to the agent; (c) followingthe exposing in step (b), measuring in said biological sample the levelof the at least one biomarker, wherein an increase in the level of theat least one biomarker measured in step (c) compared to the level of theat least one biomarker measured in step (a), predicts that the mammalwill respond therapeutically to said method of treating cancer when saidbiomarker is from Table 1, and predicts that the mammal will not respondtherapeutically to said method of treating cancer when said biomarker isfrom Table 2.

In another aspect, the invention provides a method for determiningwhether a mammal is responding therapeutically to amicrotubule-stabilizing agent, comprising (a) exposing the mammal to theagent; and (b) following the exposing of step (a), measuring in themammal the level of at least one biomarker selected from the biomarkersof Table 1 and Table 2, wherein an increase in the level of the at leastone biomarker measured in step (b), compared to the level of the atleast one biomarker in a mammal that has not been exposed to said agent,indicates that the mammal is responding to said agent when saidbiomarker is from Table 1, and indicates that the mammal is notresponding to said agent when said biomarker is from Table 2.

In another aspect, the invention provides a method for predictingwhether a mammal will respond therapeutically to a method of treatingcancer comprising administering a microtubule-stabilizing agent, whereinthe method comprises: (a) exposing a biological sample from the mammalto the microtubule-stabilizing agent; (b) following the exposing of step(a), measuring in said biological sample the level of at least onebiomarker selected from the biomarkers of Table 1 or Table 2, wherein anincrease in the level of the at least one biomarker measured in step(b), compared to the level of the at least one biomarker in a mammalthat has not been exposed to said agent, predicts that the mammal willrespond therapeutically to said method of treating cancer when saidbiomarker is from Table 1, and predicts that the mammal will not respondtherapeutically to said method of treating cancer when said biomarker isfrom Table 2.

In another aspect, the invention provides a method for determiningwhether an agent stabilizes microtubules and has cytotoxic activityagainst rapidly proliferating cells, such as, tumor cells or otherhyperproliferative cellular disease in a mammal, comprising: (a)exposing the mammal to the agent; and (b) following the exposing of step(a), measuring in the mammal the level of at least one biomarkerselected from the biomarkers of Table 1 and Table 2, wherein an increasein the level of said at least one biomarker measured in step (b),compared to the level of the biomarker in a mammal that has not beenexposed to said agent, indicates that the agent stabilizes microtubulesand has cytotoxic activity against rapidly proliferating cells when saidbiomarker is from Table 1, and indicates that the agent does notstabilize microtubules and does not have cytotoxic activity againstrapidly proliferating cells when said biomarker is from Table 2.

As used herein, respond therapeutically refers to the alleviation orabrogation of the cancer. This means that the life expectancy of anindividual affected with the cancer will be increased or that one ormore of the symptoms of the cancer will be reduced or ameliorated. Theterm encompasses a reduction in cancerous cell growth or tumor volume.Whether a mammal responds therapeutically can be measured by manymethods well known in the art, such as PET imaging.

The amount of increase in the level of the at least one biomarkermeasured in the practice of the invention can be readily determined byone skilled in the art. In one aspect, the increase in the level of abiomarker is at least a two-fold difference, at least a three-folddifference, or at least a four-fold difference in the level of thebiomarker.

The mammal can be, for example, a human, rat, mouse, dog, rabbit, pigsheep, cow, horse, cat, primate, or monkey.

The method of the invention can be, for example, an in vitro methodwherein the step of measuring in the mammal the level of at least onebiomarker comprises taking a biological sample from the mammal and thenmeasuring the level of the biomarker(s) in the biological sample. Thebiological sample can comprise, for example, at least one of whole freshblood, peripheral blood mononuclear cells, frozen whole blood, freshplasma, frozen plasma, urine, saliva, skin, hair follicle, bone marrow,or tumor tissue.

The level of the at least one biomarker can be, for example, the levelof protein and/or mRNA transcript of the biomarker(s).

The invention also provides an isolated biomarker selected from thebiomarkers of Table 1 and Table 2. The biomarkers of the inventioncomprise sequences selected from the nucleotide and amino acid sequencesprovided in Table 1 and Table 2 and the Sequence Listing, as well asfragments and variants thereof.

The invention also provides a biomarker set comprising two or morebiomarkers selected from the biomarkers of Table 1 and Table 2.

The invention also provides kits for determining or predicting whether apatient would be susceptible or resistant to a treatment that comprisesone or more microtubule-stabilizing agents. The patient may have acancer or tumor such as, for example, a breast cancer or tumor.

In one aspect, the kit comprises a suitable container that comprises oneor more specialized microarrays of the invention, one or moremicrotubule-stabilizing agents for use in testing cells from patienttissue specimens or patient samples, and instructions for use. The kitmay further comprise reagents or materials for monitoring the expressionof a biomarker set at the level of mRNA or protein.

In another aspect, the invention provides a kit comprising two or morebiomarkers selected from the biomarkers of Table 1 and Table 2.

In yet another aspect, the invention provides a kit comprising at leastone of an antibody and a nucleic acid for detecting the presence of atleast one of the biomarkers selected from the biomarkers of Table 1 andTable 2. In one aspect, the kit further comprises instructions fordetermining whether or not a mammal will respond therapeutically to amethod of treating cancer comprising administering amicrotubule-stabilizing agent. In another aspect, the instructionscomprise the steps of (a) measuring in the mammal the level of at leastone biomarker selected from the biomarkers of Table 1 and Table 2, (b)exposing the mammal to the microtubule-stabilizing agent, (c) followingthe exposing of step (b), measuring in the mammal the level of the atleast one biomarker, wherein a difference in the level of the at leastone biomarker measured in step (c) compared to the level of the at leastone biomarker measured in step (a) predicts that the mammal will respondtherapeutically to said method of treating cancer when said biomarker isfrom Table 1, and predicts that the mammal will not respondtherapeutically to said method of treating cancer when said biomarker isfrom Table 2.

The invention also provides screening assays for determining if apatient will be susceptible or resistant to treatment with one or moremicrotubule-stabilizing agents.

The invention also provides a method of monitoring the treatment of apatient having a disease, wherein said disease is treated by a methodcomprising administering one or more microtubule-stabilizing agents.

The invention also provides individualized genetic profiles which arenecessary to treat diseases and disorders based on patient response at amolecular level.

The invention also provides specialized microarrays, e.g.,oligonucleotide microarrays or cDNA microarrays, comprising one or morebiomarkers having expression profiles that correlate with eithersensitivity or resistance to one or more microtubule-stabilizing agents.

The invention also provides antibodies, including polyclonal ormonoclonal, directed against one or more biomarkers of the invention.

The invention will be better understood upon a reading of the detaileddescription of the invention when considered in connection with theaccompanying figures.

BRIEF DESCRIPTION OF THE FIGURES

The patent or application file contains at least one drawing executed incolor. Copies of this patent or patent application publication withcolor drawing(s) will be provided by the Office upon request and paymentof the necessary fee.

FIG. 1 illustrates classification of breast cancer cell lines based onIC₅₀ values measured against ixabepilone treatment. The cell lines werenormalized based on a mean of the log(IC₅₀) values (a dotted line) anddivided into two groups defined as sensitive or resistant. The celllines on the left are defined as sensitive since they are below the meanof the log(IC₅₀)s, and those on the right are defined as resistant sincethey are above the mean.

FIG. 2 illustrates the error rates generated from each classifieridentified. From the GeneCluster analysis, classifiers containing up to250 genes were determined. Each predictor identified was evaluated withthe error rate calculated through the leave-one out cross validation. Asshown in FIG. 2, error rates for classifiers (8-250 genes) remain to bethe minimum at zero.

FIG. 3 illustrates the error rate calculation on random permutation.Error rates generated from several examples of random classification(random 1-11) using the software GeneCluster are plotted against thepredictor sets containing up to 250 genes. As shown in the plot, theerror rate calculated based on the IC₅₀-based classification issignificantly lower than the error rates based on the randomclassification.

FIG. 4 illustrates the top 50 genes correlated with sensitivity forixabepilone. The red and blue matrix represents the normalizedexpression patterns for each gene across the cell lines (brightest redindicates highest relative expression, darkest blue indicates lowestrelative expression).

FIG. 5 illustrates gene expression level of microtubule associatedprotein, tau and estrogen receptor (also referred to herein as estrogenreceptor 1, ER, and ER1). In order to explore the relationship betweenTau and ER, gene expression levels of the two are plotted for each cellline. Tau expression levels are shown as a bar, and ER as a line.

FIG. 6 illustrates gene expression patterns of top 50 genes in 175primary breast tumors. The red and green matrix represents thenormalized expression patterns for each gene across the 175 primarybreast tumors (brightest red indicates highest relative expression,green indicates lowest relative expression). A subset of tumors in ablue box shows relative high expression of the top 25 markers whichexpressed highly in the sensitive cell lines. On the other hand, thetumors in a magenta box show relatively high expression of the 25 genesexpressed at elevated levels in the resistant cell lines.

FIG. 7 illustrates MAP tau and ER expression in breast tumors. In orderto see the expression patterns of Tau and ER within tumors, theirexpression levels are plotted together. Tau is shown as a line, and ERas a bar. Tumors are arranged in an increasing order of Tau expressionlevel. There seems to be a subset of tumors that express these geneshighly, which suggest these are non-responders for ixabepilone.

FIG. 8 illustrates the biological networks implied in the mechanism ofresistance to ixabepilone as determined by Ingenuity® pathway analysisusing 200 preclinical candidate markers. There are nine major networksindicated above with their significance scores. As shown, ER pathway isthe most implicated network.

FIG. 9 illustrates the most implicated ER network and shows thefunctional connectivity between ER and Tau.

FIG. 10 illustrates molecular intrinsic profiles of 134 patient tumors.A hierarchical clustering analysis was performed using about 9800 genesafter eliminating low expressed and low variance genes. Row, gene;column, tumor. The tumors were classified into two major clusters and,interestingly, the majority of the samples from three Russian sites wereclustered in the first cluster.

DETAILED DESCRIPTION OF THE INVENTION

The invention provides biomarkers that correlate withmicrotubule-stabilization agent sensitivity or resistance. Thesebiomarkers can be employed for predicting response to one or moremicrotubule-stabilization agents. In one aspect, the biomarkers of theinvention are those provided in Table 1, Table 2, and the SequenceListing, including both polynucleotide and polypeptide sequences.

The biomarkers provided in Table 1 include the nucleotide sequences ofSEQ ID NOS:1-100 and the amino acid sequences of SEQ ID NOS:201-299.

TABLE 1 BIOMARKERS (SENSITIVE) Affymetrix Unigene title and Probe GeneSEQ ID NO: Affymetrix Description Set Ontology C6orf145: “Consensusincludes gb: AK024828.1 212923_s_at chromosome 6 /DEF = Homo sapienscDNA: FLJ21175 open reading fis, clone CAS11071. /FEA = mRNA frame 145/DB_XREF = gi: 10437233 (LOC221749) /UG = Hs.69388 hypothetical proteinSEQ ID NOS: 1 FLJ20505” (DNA) and 201 (amino acid) RTCD1: RNA “gb:NM_003729.1 /DEF = Homo sapiens 203594_at assembly terminal phosphateRNA 3-terminal phosphate cyclase of cyclase domain 1 (RPC), mRNA. /FEA =mRNA spliceosomal (LOC8634) /GEN = RPC /PROD = RNA 3-terminal tri- SEQID NOS: 2 phosphate cyclase snRNP (DNA) and 202 /DB_XREF = gi: 4506588/UG = Hs.27076 (amino acid) RNA 3-terminal phosphate cyclase /FL = gb:NM_003729.1” FXYD5: FXYD “gb: NM_014164.2 /DEF = Homo sapiens218084_x_at negative domain containing FXYD domain-containing iontransport regulation ion transport regulator 5 (FXYD5), mRNA. ofregulator 5 /FEA = mRNA /GEN = FXYD5 calcium- (LOC53827) /PROD = relatedto ion channel dependent SEQ ID NOS: 3 /DB_XREF = gi: 11612664 cell-cell(DNA) and 203 /UG = Hs.294135 FXYD domain- adhesion (amino acid)containing ion transport regulator 5 /FL = gb: NM_014164.2 gb:AF161462.1” G3BP: Ras- Consensus includes gb: BG500067 201503_atprotein- GTPase-activating /FEA = EST /DB_XREF = gi: 13461584 nucleusprotein SH3- /DB_XREF = est: 602545874F1 import domain-binding /CLONE =IMAGE: 4668234 protein /UG = Hs.220689 Ras-GTPase-activating (LOC10146)protein SH3-domain-binding protein SEQ ID NOS: 4 /FL = gb: U32519.1 gb:NM_005754.1 (DNA) and 204 (amino acid) FKBP1A: FK506 “gb: NM_000801.1/DEF = Homo sapiens 200709_at protein binding protein FK506-bindingprotein 1A (12 kD) folding 1A, 12 kDa (FKBP1A), mRNA. /FEA = mRNA(LOC2280) /GEN = FKBP1A /PROD = FK506-binding SEQ ID NOS: 5 protein 1A(12 kD) (DNA) and 205 /DB_XREF = gi: 4503724 /UG = Hs.752 (amino acid)FK506-binding protein 1A (12 kD) /FL = gb: BC001925.1 gb: M34539.1 gb:NM_000801.1” VARS2: valyl- “gb: NM_006295.1 /DEF = Homo sapiens201797_s_at translational tRNA synthetase 2 valyl-tRNA synthetase 2(VARS2), elongation (LOC7407) mRNA. /FEA = mRNA /GEN = VARS2 SEQ ID NOS:6 /PROD = valyl-tRNA synthetase 2 (DNA) and 206 /DB_XREF = gi: 5454157(amino acid) /UG = Hs.159637 valyl-tRNA synthetase 2 /FL = gb:NM_006295.1” FKBP1A: FK506 Consensus includes gb: AI936769 214119_s_atprotein binding protein /FEA = EST /DB_XREF = gi: 5675639 folding 1A, 12kDa /DB_XREF = est: wp69c11.x1 (LOC2280) /CLONE = IMAGE: 2467028 /UG =Hs.752 SEQ ID NOS: 7 FK506-binding protein 1A (12 kD) (DNA) and 207(amino acid) MTMR2: “Consensus includes gb: AK027038.1 203211_s_atprotein myotubularin /DEF = Homo sapiens cDNA: FLJ23385 amino relatedprotein 2 fis, clone HEP16802. /FEA = mRNA acid (LOC8898) /DB_XREF = gi:10440053 dephosphorylation SEQ ID NOS: 8 /UG = Hs.181326 KIAA1073protein (DNA) and 208 /FL = gb: AB028996.1 gb: NM_016156.1” (amino acid)PSMB8: “gb: U17496.1 /DEF = Human proteasome 209040_s_at proteolysisproteasome subunit LMP7 (allele LMP7B) mRNA, and (prosome, complete cds./FEA = mRNA peptidolysis, macropain) /GEN = LMP7 /PROD = proteasomeubiquitin- subunit, beta type, subunit LMP7 /DB_XREF = gi: 596139dependent 8 (large /UG = Hs.180062 proteasome (prosome, proteinmultifunctional macropain) subunit, beta type, 8 (large catabolismprotease 7) multifunctional protease 7) (LOC5696) /FL = gb: U17496.1 gb:U17497.1” SEQ ID NOS: 9 (DNA) and 209 (amino acid) CTSC: cathepsin C“gb: NM_001814.1 /DEF = Homo sapiens 201487_at proteolysis (LOC1075)cathepsin C (CTSC), mRNA. and SEQ ID NOS: 10 /FEA = mRNA /GEN = CTSCpeptidolysis (DNA) and 210 /PROD = cathepsin C (amino acid) /DB_XREF =gi: 4503140 /UG = Hs.10029 cathepsin C /FL = gb: NM_001814.1” ST5:suppression “gb: NM_005418.1 /DEF = Homo sapiens 202440_s_at oftumorigenicity 5 suppression of tumorigenicity 5 (ST5), (LOC6764) mRNA./FEA = mRNA /GEN = ST5 SEQ ID NOS: 11 /PROD = suppression oftumorigenicity 5 (DNA) and 211 /DB_XREF = gi: 4885612 /UG = Hs.79265(amino acid) suppression of tumorigenicity 5 /FL = gb: U15131.1 gb:U15779.1 gb: NM_005418.1” MTMR2: “Consensus includes gb: U58033.1214649_s_at protein myotubularin /DEF = Homo sapiens myotubularin aminorelated protein 2 related protein 2 (MTMR2) mRNA, acid (LOC8898) partialcds. /FEA = mRNA dephosphorylation SEQ ID NOS: 12 /GEN = MTMR2 /PROD =myotubularin (DNA) and 212 related protein 2 /DB_XREF = gi: 3912941(amino acid) /UG = Hs.278491 myotubularin related protein 2 /FL = gb:NM_003912.1” PRNP: prion “gb: NM_000311.1 /DEF = Homo sapiens201300_s_at protein (p27-30) prion protein (p27-30) (Creutzfeld-Jakob(Creutzfeld-Jakob disease, Gerstmann-Strausler-Scheinker disease,syndrome, fatal familial insomnia) Gerstmann- (PRNP), mRNA. /FEA = mRNAStrausler- /GEN = PRNP /PROD = prion protein Scheinker /DB_XREF = gi:4506112 /UG = Hs.74621 syndrome, fatal prion protein (p27-30)(Creutzfeld-Jakob familial insomnia) disease,Gerstmann-Strausler-Scheinker (LOC5621) syndrome, fatal familialinsomnia) SEQ ID NOS: 13 /FL = gb: AY008282.1 gb: M13899.1 (DNA) and 213gb: NM_000311.1” (amino acid) MET: met proto- “gb: U19348.1 /DEF = Human(tpr-met 211599_x_at signal oncogene fusion) oncogene mRNA, completecds. transduction (hepatocyte /FEA = mRNA /GEN = tprmet fusion growthfactor /PROD = tpr-met fusion protein receptor) /DB_XREF = gi: 625085(LOC4233) /FL = gb: U19348.1” SEQ ID NOS: 14 (DNA) and 214 (amino acid)MIRAB13: “Cluster Incl. W46406: zc31c10.s1 Homo 55081_at vesicle-molecule sapiens cDNA, 3 end /clone = IMAGE- mediated interacting with323922 /clone_end = 3′ /gb = W46406 transport Rab13 /gi = 1331036 /ug =Hs.8535 /len = 568” (LOC85377) SEQ ID NOS: 15 (DNA) and 215 (amino acid)AKAP2: A kinase Consensus includes gb: BE879367 202759_s_at (PRKA)anchor /FEA = EST /DB_XREF = gi: 10328143 protein 2 /DB_XREF = est:601484628F1 (LOC11217) /CLONE = IMAGE: 3887262 SEQ ID NOS: 16 /UG =Hs.42322 A kinase (PRKA) anchor (DNA) and 216 protein 2 /FL = gb:AB023137.1 (amino acid) gb: NM_007203.1 MET: met proto- Consensusincludes gb: BG170541 203510_at signal oncogene /FEA = EST /DB_XREF =gi: 12677244 transduction (hepatocyte /DB_XREF = est: 602322942F1 growthfactor /CLONE = IMAGE: 4425947 receptor) /UG = Hs.285754 metproto-oncogene (LOC4233) (hepatocyte growth factor receptor) SEQ ID NOS:17 /FL = gb: J02958.1 gb: NM_000245.1 (DNA) and 217 (amino acid) STAC:SH3 and “gb: NM_003149.1 /DEF = Homo sapiens 205743_at intracellularcysteine rich src homology three (SH3) and cysteine signaling domainrich domain (STAC), mRNA. cascade (LOC6769) /FEA = mRNA /GEN = STAC/PROD = src SEQ ID NOS: 18 homology three (SH3) and cysteine (DNA) and218 richdomain /DB_XREF = gi: 4507246 (amino acid) /UG = Hs.56045 srchomology three (SH3) and cysteine rich domain /FL = gb: D86640.1 gb:NM_003149.1” CALU: calumenin Consensus includes gb: BF939365 200755_s_at(LOC813) /FEA = EST /DB_XREF = gi: 12356685 SEQ ID NOS: 19 /DB_XREF =est: nad87h04.x1 (DNA) and 219 /CLONE = IMAGE: 3410551 (amino acid) /UG= Hs.7753 calumenin /FL = gb: U67280.1 gb: AF013759.1 gb: NM_001219.2MSN: moesin “gb: NM_002444.1 /DEF = Homo sapiens 200600_at cell(LOC4478) moesin (MSN), mRNA. /FEA = mRNA motility SEQ ID NOS: 20 /GEN =MSN /PROD = moesin (DNA) and 220 /DB_XREF = gi: 4505256 (amino acid) /UG= Hs.170328 moesin /FL = gb: M69066.1 gb: NM_002444.1” ANXA1: annexin“gb: NM_000700.1 /DEF = Homo sapiens 201012_at inflammatory A1 (LOC301)annexin A1 (ANXA1), mRNA. response, SEQ ID NOS: 21 /FEA = mRNA /GEN =ANXA1 cell (DNA) and 221 /PROD = annexin I motility (amino acid)/DB_XREF = gi: 4502100 /UG = Hs.78225 annexin A1 /FL = gb: BC001275.1gb: NM_000700.1” CGI-100: CGI-100 “gb: NM_016040.1 /DEF = Homo sapiens202195_s_at intracellular protein CGI-100 protein (LOC50999), mRNA.protein (LOC50999) /FEA = mRNA /GEN = LOC50999 transport SEQ ID NOS: 22/PROD = CGI-100 protein (DNA) and 222 /DB_XREF = gi: 7705583 (aminoacid) /UG = Hs.296155 CGI-100 protein /FL = gb: AF151858.1 gb:NM_016040.1” CALU: calumenin “gb: NM_001219.2 /DEF = Homo sapiens200757_s_at (LOC813) calumenin (CALU), mRNA. SEQ ID NOS: 23 /FEA = mRNA/GEN = CALU (DNA) and 223 /PROD = calumenin precursor (amino acid)/DB_XREF = gi: 6005991 /UG = Hs.7753 calumenin /FL = gb: U67280.1 gb:AF013759.1 gb: NM_001219.2” EGFR: epidermal “gb: U95089.1 /DEF = Humantruncated 210984_x_at EGF growth factor epidermal growth factorreceptor-like receptor receptor protein precursor mRNA, complete cds.signaling (erythroblastic /FEA = mRNA /PROD = truncated pathway leukemiaviral (v- epidermal growth factor receptor- erb-b) oncogene likeproteinprecursor homolog, avian) /DB_XREF = gi: 2051984 /UG = Hs.77432(LOC1956) epidermal growth factor receptor (avian SEQ ID NOS: 24erythroblastic leukemia viral (v-erb-b) (DNA) and 224 oncogene homolog)/FL = gb: U95089.1” (amino acid) CASP4: caspase 4, “gb: U25804.1 /DEF =Human Ich-2 209310_s_at apoptosis apoptosis-related cysteine proteasemRNA, complete cds. cysteine protease /FEA = mRNA /PROD = Ich-2 (LOC837)/DB_XREF = gi: 886049 /UG = Hs.74122 SEQ ID NOS: 25 caspase 4,apoptosis-related cysteine (DNA) and 225 protease /FL = gb: U28976.1 gb:U28977.1 (amino acid) gb: U28978.1 gb: NM_001225.1 gb: U25804.1 gb:U28014.1” DKFZP566E144: “gb: NM_015523.1 /DEF = Homo sapiens 218194_atnucleotide small fragment small fragment nuclease metabolism nuclease(DKFZP566E144), mRNA. (LOC25996) /FEA = mRNA /GEN = DKFZP566E144 SEQ IDNOS: 26 /PROD = small fragment nuclease (DNA) and 226 /DB_XREF = gi:7661645 /UG = Hs.7527 (amino acid) small fragment nuclease /FL = gb:AF151872.1 gb: AL110239.1 gb: NM_015523.1” AKR1B1: aldo- “gb:NM_001628.1 /DEF = Homo sapiens 201272_at carbohydrate keto reductasealdo-keto reductase family 1, member B1 metabolism family 1, member(aldose reductase) (AKR1B1), mRNA. B1 (aldose /FEA = mRNA /GEN = AKR1B1reductase) /PROD = aldo-keto reductase family 1, (LOC231) member B1(aldosereductase) SEQ ID NOS: 27 /DB_XREF = gi: 4502048 /UG = Hs.75313(DNA) and 227 aldo-keto reductase family 1, member B1 (amino acid)(aldose reductase) /FL = gb: BC000260.1 gb: BC005387.1 gb: J04795.1 gb:J05017.1 gb: J05474.1 gb: M34720.1 gb: NM_001628.1” CAV1: caveolin 1,Consensus includes gb: AU147399 212097_at caveolae protein, /FEA = EST/DB_XREF = gi: 11008920 22 kDa (LOC857) /DB_XREF = est: AU147399 SEQ IDNOS: 28 /CLONE = MAMMA1000563 (DNA) and 228 /UG = Hs.74034 Homo sapiensclone (amino acid) 24651 mRNA sequence MBNL2: Consensus includes gb:BE328496 203640_at muscleblind-like 2 /FEA = EST /DB_XREF = gi: 9202272(Drosophila) /DB_XREF = est: hs98f09.x1 (LOC10150) /CLONE = IMAGE:3145289 SEQ ID NOS: 29 /UG = Hs.283609 hypothetical protein (DNA) and229 PRO2032 /FL = gb: AF116683.1 (amino acid) gb: NM_018615.1 CRSP6:cofactor “gb: AF105421.1 /DEF = Homo sapiens 221517_s_at regulationrequired for Sp1 vitamin D3 receptor interacting protein oftranscriptional (DRIP80) mRNA, complete cds. transcription, activation,subunit /FEA = mRNA /GEN = DRIP80 DNA- 6, 77 kDa /PROD = vitamin D3receptor interacting dependent (LOC9440) protein /DB_XREF = gi: 4838128SEQ ID NOS: 30 /UG = Hs.22630 cofactor required for Sp1 (DNA) and 230transcriptional activation, subunit 6 (amino acid) (77 kD) /FL = gb:AF105421.1” CALU: calumenin “gb: U67280.1 /DEF = Homo sapiens200756_x_at (LOC813) calumenin mRNA, complete cds. SEQ ID NOS: 31 /FEA =mRNA /PROD = calumenin (DNA) and 231 /DB_XREF = gi: 2809323 /UG =Hs.7753 (amino acid) calumenin /FL = gb: U67280.1 gb: AF013759.1 gb:NM_001219.2” PTRF: polymerase “Consensus includes gb: BC004295.1208789_at I and transcript /DEF = Homo sapiens, clone release factorIMAGE: 3622356, mRNA, partial cds. (LOC284119) /FEA = mRNA /PROD =Unknown SEQ ID NOS: 32 (protein for IMAGE: 3622356) (DNA) and 232/DB_XREF = gi: 13279151 (amino acid) /UG = Hs.29759 RNA POLYMERASE I ANDTRANSCRIPT RELEASE FACTOR /FL = gb: AF312393.1” NUP155: “gb: NM_004298.1/DEF = Homo sapiens 206550_s_at nucleocytoplasmic nucleoporinnucleoporin 155 kD (NUP155), mRNA. transport 155 kDa /FEA = mRNA /GEN =NUP155 (LOC9631) /PROD = nucleoporin 155 kD SEQ ID NOS: 33 /DB_XREF =gi: 4758843 /UG = Hs.23255 (DNA) and 233 nucleoporin 155 kD /FL = gb:AB018334.1 (amino acid) gb: NM_004298.1” DONSON: “gb: AF232674.1 /DEF =Homo sapiens 221677_s_at downstream B17 mRNA, complete cds. /FEA = mRNAneighbor of SON /PROD = B17 /DB_XREF = gi: 8118230 (LOC29980) /UG =Hs.17834 downstream neighbor of SEQ ID NOS: 34 SON /FL = gb: AF232674.1”(DNA) and 234 (amino acid) CALU: calumenin “Consensus includes gb:AF257659.1 214845_s_at (LOC813) /DEF = Homo sapiens crocalbin-like SEQID NOS: 35 protein mRNA, partial cds. (DNA) and 235 /FEA = mRNA /PROD =crocalbin-like (amino acid) protein /DB_XREF = gi: 8515717 /UG =Hs.302073 Homo sapiens crocalbin-like protein mRNA, partial cds” FAD104:FAD104 “gb: NM_022763.1 /DEF = Homo sapiens 218618_s_at (LOC64778)hypothetical protein FLJ23399 SEQ ID NOS: 36 (FLJ23399), mRNA. /FEA =mRNA (DNA) and 236 /GEN = FLJ23399 /PROD = hypothetical (amino acid)protein FLJ23399 /DB_XREF = gi: 12232434 /UG = Hs.299883 hypotheticalprotein FLJ23399 /FL = gb: NM_022763.1” EPHA2: EphA2 “gb: NM_004431.1/DEF = Homo sapiens 203499_at (LOC1969) EphA2 (EPHA2), mRNA. /FEA = mRNASEQ ID NOS: 37 /GEN = EPHA2 /PROD = EphA2 (DNA) and 237 /DB_XREF = gi:4758277 (amino acid) /UG = Hs.171596 EphA2 /FL = gb: M59371.1 gb:NM_004431.1” PAK1IP1: PAK1 “gb: NM_017906.1 /DEF = Homo sapiens218886_at interacting protein hypothetical protein FLJ20624 1 (LOC55003)(FLJ20624), mRNA. /FEA = mRNA SEQ ID NOS: 38 /GEN = FLJ20624 /PROD =hypothetical (DNA) and 238 protein FLJ20624 (amino acid) /DB_XREF = gi:8923576 /UG = Hs.52256 hypothetical protein FLJ20624 /FL = gb:NM_017906.1” CTPS: CTP “gb: NM_001905.1 /DEF = Homo sapiens 202613_atpyrimidine synthase CTP synthase (CTPS), mRNA. nucleotide (LOC1503) /FEA= mRNA /GEN = CTPS biosynthesis SEQ ID NOS: 39 /PROD = CTP synthase(DNA) and 239 /DB_XREF = gi: 4503132 (amino acid) /UG = Hs.251871 CTPsynthase /FL = gb: NM_001905.1” CD44: CD44 “gb: BC004372.1 /DEF = Homosapiens, 209835_x_at cell-cell antigen (homing Similar to CD44 antigen(homing adhesion function and function and Indian blood group system),Indian blood group clone MGC: 10468, mRNA, complete system) (LOC960)cds. /FEA = mRNA /PROD = Similar to SEQ ID NOS: 40 CD44 antigen (homingfunction (DNA) and 240 andIndian blood group system) (amino acid)/DB_XREF = gi: 13325117 /UG = Hs.169610 CD44 antigen (homing functionand Indian blood group system) /FL = gb: BC004372.1” CD97: CD97 “gb:NM_001784.1 /DEF = Homo sapiens 202910_s_at G-protein antigen (LOC976)CD97 antigen (CD97), mRNA. coupled SEQ ID NOS: 41 /FEA = mRNA /GEN =CD97 receptor (DNA) and 241 /PROD = CD97 antigen protein (amino acid)/DB_XREF = gi: 4502690./UG = Hs.3107 signaling CD97 antigen /FL = gb:NM_001784.1” pathway SPTBN1: spectrin, “Consensus includes gb: BE968833212071_s_at beta, non- /FEA = EST /DB_XREF = gi: 10579538 erythrocytic 1/DB_XREF = est: 601649861F1 (LOC6711) /CLONE = IMAGE: 3933782 SEQ IDNOS: 42 /UG = Hs.324648 Homo sapiens cDNA (DNA) and 242 FLJ13700 fis,clone PLACE2000216, (amino acid) highly similar to SPECTRIN BETA CHAIN,BRAIN” SH3GLB1: SH3- “gb: AF263293.1 /DEF = Homo sapiens 209091_s_atdomain GRB2-like endophilin B1 mRNA, complete cds. endophilin B1 /FEA =mRNA /PROD = endophilin B1 (LOC51100) /DB_XREF = gi: 8118529 SEQ ID NOS:43 /UG = Hs.136309 SH3-containing protein (DNA) and 243 SH3GLB1 /FL =gb: AF263293.1” (amino acid) PGM1: “gb: NM_002633.1 /DEF = Homo sapiens201968_s_at glucose phosphoglucomutase phosphoglucomutase 1 (PGM1),mRNA. metabolism 1 (LOC5236) /FEA = mRNA /GEN = PGM1 SEQ ID NOS: 44/PROD = phosphoglucomutase 1 (DNA) and 244 /DB_XREF = gi: 4505764 /UG =Hs.1869 (amino acid) phosphoglucomutase 1 /FL = gb: BC001756.1 gb:M83088.1 gb: NM_002633.1” SH3GLB1: SH3- “gb: AF257318.1 /DEF = Homosapiens 210101_x_at domain GRB2-like SH3-containing protein SH3GLB1endophilin B1 mRNA, complete cds. /FEA = mRNA (LOC51100) /PROD =SH3-containing protein SEQ ID NOS: 45 SH3GLB1 /DB_XREF = gi: 8896091(DNA) and 245 /UG = Hs.136309 SH3-containing protein (amino acid)SH3GLB1 /FL = gb: AF350371.1 gb: AF151819.1 gb: NM_016009.1 gb:AF257318.1” GBP1: guanylate “gb: BC002666.1 /DEF = Homo sapiens,202269_x_at immune binding protein 1, guanylate binding protein 1,interferon- response interferon- inducible, 67 kD, clone MGC: 3949,inducible, 67 kDa mRNA, complete cds. /FEA = mRNA (LOC2633) /PROD =guanylate binding protein SEQ ID NOS: 46 1, interferon-inducible, 67 kD(DNA) and 246 /DB_XREF = gi: 12803662 (amino acid) /UG = Hs.62661guanylate binding protein 1, interferon-inducible, 67 kD /FL = gb:BC002666.1 gb: M55542.1 gb: NM_002053.1” ADORA2B: “gb: NM_000676.1 /DEF= Homo sapiens 205891_at adenylate adenosine A2b adenosine A2b receptor(ADORA2B), cyclase receptor (LOC136) mRNA. /FEA = mRNA activation SEQ IDNOS: 47 /GEN = ADORA2B /PROD = adenosine (DNA) and 247 A2b receptor/DB_XREF = gi: 4501950 (amino acid) /UG = Hs.45743 adenosine A2breceptor /FL = gb: M97759.1 gb: NM_000676.1” PLS3: plastin 3 (T “gb:NM_005032.2 /DEF = Homo sapiens 201215_at isoform) plastin 3 (T isoform)(PLS3), mRNA. (LOC5358) /FEA = mRNA /GEN = PLS3 SEQ ID NOS: 48 /PROD =plastin 3 precursor (DNA) and 248 /DB_XREF = gi: 7549808 /UG = Hs.4114(amino acid) plastin 3 (T isoform) /FL = gb: M22299.1 gb: NM_005032.2”PDGFC: platelet “gb: NM_016205.1 /DEF = Homo sapiens 218718_at derivedgrowth platelet derived growth factor C factor C (PDGFC), mRNA. /FEA =mRNA (LOC56034) /GEN = PDGFC /PROD = secretory growth SEQ ID NOS: 49factor-like protein fallotein (DNA) and 249 /DB_XREF = gi: 9994186 /UG =Hs.43080 (amino acid) platelet derived growth factor C /FL = gb:AF091434.1 gb: AF244813.1 gb: AB033831.1 gb: NM_016205.1” MID1: midline1 “gb: NM_000381.1 /DEF = Homo sapiens 203637_s_at microtubule(Opitz/BBB midline 1 (OpitzBBB syndrome) cytoskeleton syndrome) (MID1),mRNA. /FEA = mRNA organization (LOC4281) /GEN = MID1 /PROD = midline 1and SEQ ID NOS: 50 /DB_XREF = gi: 4557752 /UG = Hs.27695 biogenesis(DNA) and 250 midline 1 (OpitzBBB syndrome) (amino acid) /FL = gb:AF269101.1 gb: AF230976.1 gb: AF035360.1 gb: NM_000381.1” MET: metproto- Consensus includes gb: BE870509 213807_x_at signal oncogene /FEA= EST /DB_XREF = gi: 10319285 transduction (hepatocyte /DB_XREF = est:601447096F1 growth factor /CLONE = IMAGE: 3851374 receptor) /UG =Hs.285754 met proto-oncogene (LOC4233) (hepatocyte growth factorreceptor) SEQ ID NOS: 51 (DNA) and 251 (amino acid) CHST6: “gb:NM_021615.1 /DEF = Homo sapiens 221059_s_at proteoglycan carbohydrate(N- carbohydrate (N-acetylglucosamine 6-O) sulfate acetylglucosaminesulfotransferase 6 (CHST6), mRNA. transfer 6-O) /FEA = mRNA /GEN = CHST6sulfotransferase 6 /PROD = carbohydrate (N- (LOC4166) acetylglucosamine6-O)sulfotransferase 6 SEQ ID NOS: 52 /DB_XREF = gi: 11055975 (DNA) and252 /UG = Hs.157439 carbohydrate (N- (amino acid) acetylglucosamine 6-O)sulfotransferase 6 /FL = gb: AF219990.1 gb: NM_021615.1” MEIS2: Meis1,“gb: NM_020149.1 /DEF = Homo sapiens 207480_s_at negative myeloidecotropic TALE homeobox protein Meis2e regulation viral integration(LOC56908), mRNA. /FEA = mRNA of site 1 homolog 2 /GEN = LOC56908 /PROD= TALE transcription (mouse) homeobox protein Meis2e from (LOC4212)/DB_XREF = gi: 9910355 Pol II SEQ ID NOS: 53 /UG = Hs.283312 TALEhomeobox promoter (DNA) and 253 protein Meis2e /FL = gb: AF179899.1(amino acid) gb: NM_020149.1” UPP1: uridine “gb: NM_003364.1 /DEF = Homosapiens 203234_at nucleoside phosphorylase 1 uridine phosphorylase (UP),mRNA. metabolism (LOC7378) /FEA = mRNA /GEN = UP /PROD = uridine SEQ IDNOS: 54 phosphorylase /DB_XREF = gi: 4507838 (DNA) and 254 /UG =Hs.77573 uridine phosphorylase (amino acid) /FL = gb: BC001405.1 gb:NM_003364.1” CD44: CD44 Consensus includes gb: AI493245 212014_x_atcell-cell antigen (homing /FEA = EST /DB_XREF = gi: 4394248 adhesionfunction and /DB_XREF = est: ti30d08.x1 Indian blood group /CLONE =IMAGE: 2131983 system) (LOC960) /UG = Hs.169610 CD44 antigen (homing SEQID NOS: 55 function and Indian blood group system) (DNA) and 255 (aminoacid) BTG3: BTG “Consensus includes gb: AI765445 213134_x_at regulationfamily, member 3 /FEA = EST /DB_XREF = gi: 5231954 of cell (LOC10950)/DB_XREF = est: wi80b08.x1 cycle SEQ ID NOS: 56 /CLONE = IMAGE: 2399607(DNA) and 256 /UG = Hs.77311 BTG family, member 3” (amino acid) FKBP1A:FK506 “gb: BC005147.1 /DEF = Homo sapiens, 210186_s_at protein bindingprotein FK506-binding protein 1A (12 kD), clone folding 1A, 12 kDa MGC:2167, mRNA, complete cds. (LOC2280) /FEA = mRNA /PROD = FK506-bindingSEQ ID NOS: 57 protein 1A (12 kD) (DNA) and 257 /DB_XREF = gi: 13477342/UG = Hs.752 (amino acid) FK506-binding protein 1A (12 kD) /FL = gb:BC005147.1” IFI16: interferon, “gb: NM_005531.1 /DEF = Homo sapiens206332_s_at gamma-inducible interferon, gamma-inducible protein 16protein 16 (IFI16), mRNA. /FEA = mRNA (LOC3428) /GEN = IFI16 /PROD =interferon, gamma- SEQ ID NOS: 58 inducible protein 16 (DNA) and 258/DB_XREF = gi: 5031778 (amino acid) /UG = Hs.155530 interferon, gamma-inducible protein 16 /FL = gb: M63838.1 gb: NM_005531.1” CD44: CD44Consensus includes gb: BE903880 212063_at cell-cell antigen (homing /FEA= EST /DB_XREF = gi: 10395551 adhesion function and /DB_XREF = est:601494678F1 Indian blood group /CLONE = IMAGE: 3896970 system) (LOC960)/UG = Hs.323950 zinc finger protein 6 SEQ ID NOS: 59 (CMPX1) (DNA) and259 (amino acid) IFI16: interferon, “gb: AF208043.1 /DEF = Homo sapiens208966_x_at gamma-inducible IFI16b (IFI16b) mRNA, complete cds. protein16 /FEA = mRNA /GEN = IFI16b (LOC3428) /PROD = IFI16b /DB_XREF = gi:6644296 SEQ ID NOS: 60 /UG = Hs.155530 interferon, gamma- (DNA) and 260inducible protein 16 (amino acid) /FL = gb: AF208043.1” GNG12: guanineConsensus includes gb: BG111761 212294_at signal nucleotide binding /FEA= EST /DB_XREF = gi: 12605267 transduction protein (G /DB_XREF = est:602285343F1 protein), gamma /CLONE = IMAGE: 4372619 12 (LOC55970) /UG =Hs.8107 Homo sapiens mRNA; SEQ ID NOS: 61 cDNA DKFZp586B0918 (from clone(DNA) and 261 DKFZp586B0918) (amino acid) GSTP1: “gb: NM_000852.2 /DEF =Homo sapiens 200824_at metabolism glutathione S- glutathioneS-transferase pi (GSTP1), transferase pi mRNA. /FEA = mRNA /GEN = GSTP1(LOC2950) /PROD = glutathione transferase SEQ ID NOS: 62 /DB_XREF = gi:6552334 (DNA) and 262 /UG = Hs.226795 glutathione S- (amino acid)transferase pi /FL = gb: U62589.1 gb: U30897.1 gb: NM_000852.2” MCAM:“gb: BC006329.1 /DEF = Homo sapiens, 211042_x_at melanoma cell Similarto melanoma adhesion molecule, adhesion molecule clone MGC: 12808, mRNA,complete (LOC4162) cds. /FEA = mRNA /PROD = Similar to SEQ ID NOS: 63melanoma adhesion molecule (DNA) and 263 /DB_XREF = gi: 13623456 (aminoacid) /FL = gb: BC006329.1” MIRAB13: “Consensus includes gb: BC001090.1221779_at vesicle- molecule /DEF = Homo sapiens, clone mediatedinteracting with IMAGE: 3504989, mRNA, partial cds. transport Rab13 /FEA= mRNA /PROD = Unknown (LOC85377) (protein for IMAGE: 3504989) SEQ IDNOS: 64 /DB_XREF = gi: 12654518 /UG = Hs.8535 (DNA) and 264 hypotheticalprotein bA395L14.2” (amino acid) IFI16: interferon, “Consensus includesgb: BG256677 208965_s_at gamma-inducible /FEA = EST /DB_XREF = gi:12766493 protein 16 /DB_XREF = est: 602370865F1 (LOC3428) /CLONE =IMAGE: 4478872 SEQ ID NOS: 65 /UG = Hs.155530 interferon, gamma- (DNA)and 265 inducible protein 16 (amino acid) /FL = gb: AF208043.1”DKFZp667G2110: “Consensus includes gb: BE501352 214030_at hypothetical/FEA = EST /DB_XREF = gi: 9703760 protein /DB_XREF = est: 7a41e05.x1DKFZp667G2110 /CLONE = IMAGE: 3221312 (LOC131544) /UG = Hs.23294 ESTs,Weakly similar to SEQ ID NOS: 66 T15138 hypothetical protein T28F2.4-(DNA) Caenorhabditis elegans C. elegans” C1GALT1: core 1 “gb:NM_020156.1 /DEF = Homo sapiens 219439_at UDP-galactose:N- core1UDP-galactose:N- acetylgalactosamine- acetylgalactosamine-alpha-R beta1,3- alpha-R beta 1,3- galactosyltransferase (C1GALT1),galactosyltransferase mRNA. /FEA = mRNA (LOC56913) /GEN = C1GALT1 /PROD= core1UDP- SEQ ID NOS: 67 galactose:N-acetylgalactosamine-alpha-R (DNA)and 266 beta1,3-galactosyltransferase (amino acid) /DB_XREF = gi:9910143 /UG = Hs.46744 core1 UDP-galactose:N-acetylgalactosamine-alpha-R beta 1,3- galactosyltransferase /FL = gb:AF155582.1 gb: NM_020156.1” RANGNRF: RAN “gb: NM_014185.1 /DEF = Homosapiens 218526_s_at guanine nucleotide HSPC165 protein (HSPC165), mRNA.release factor /FEA = mRNA /GEN = HSPC165 (LOC29098) /PROD = HSPC165protein SEQ ID NOS: 68 /DB_XREF = gi: 7661825 /UG = Hs.13605 (DNA) and267 HSPC165 protein /FL = gb: AF161514.1 (amino acid) gb: AF151070.1 gb:NM_014185.1 gb: NM_016492.1 gb: AF168714.1 gb: AF265206.1” ELL2:elongation “Consensus includes gb: NM_012081.1 214446_at regulationfactor, RNA /DEF = Homo sapiens ELL-RELATED of polymerase II, 2 RNAPOLYMERASE II, transcription, (LOC22936) ELONGATION FACTOR (ELL2), DNA-SEQ ID NOS: 69 mRNA. /FEA = CDS /GEN = ELL2 dependent (DNA) and 268/PROD = ELL-RELATED RNA (amino acid) POLYMERASE II, ELONGATIONFACTOR/DB_XREF = gi: 6912353 /UG = Hs.173334 ELL-RELATED RNA POLYMERASE II,ELONGATION FACTOR /FL = gb: NM_012081.1” BIN1: bridging “Consensusincludes gb: AF043899.1 214439_x_at synaptic integrator 1 /DEF = Homosapiens amphiphysin IIc1 transmission (LOC274) mRNA, complete cds. /FEA= CDS SEQ ID NOS: 70 /PROD = amphiphysin IIc1 (DNA) and 269 /DB_XREF =gi: 3064256 (amino acid) /UG = Hs.193163 bridging integrator 1 /FL = gb:AF043899.1” M-RIP: myosin “Consensus includes gb: AK025604.1 214771_x_atphosphatase-Rho /DEF = Homo sapiens cDNA: FLJ21951 interacting proteinfis, clone HEP04968. /FEA = mRNA (LOC23164) /DB_XREF = gi: 10438172 SEQID NOS: 71 /UG = Hs.84883 KIAA0864 protein” (DNA) and 270 (amino acid)MGC5306: “gb: BC001972.1 /DEF = Homo sapiens, 221580_s_at hypotheticalclone MGC: 5306, mRNA, complete cds. protein MGC5306 /FEA = mRNA /PROD =Unknown (LOC79101) (protein for MGC: 5306) SEQ ID NOS: 72 /DB_XREF = gi:12805036 (DNA) and 271 /UG = Hs.301732 hypothetical protein (amino acid)MGC5306 /FL = gb: BC001972.1” BTN3A3: “gb: NM_006994.2 /DEF = Homosapiens 204820_s_at butyrophilin, butyrophilin, subfamily 3, member A3subfamily 3, (BTN3A3), mRNA. /FEA = mRNA member A3 /GEN = BTN3A3 /PROD =butyrophilin, (LOC10384) subfamily 3, member A3 SEQ ID NOS: 73 /DB_XREF= gi: 6325463 (DNA) and 272 /UG = Hs.167741 butyrophilin, subfamily(amino acid) 3, member A3 /FL = gb: U90548.1 gb: NM_006994.2” CAV2:caveolin 2 “gb: NM_001233.1 /DEF = Homo sapiens 203324_s_at (LOC858)caveolin 2 (CAV2), mRNA. SEQ ID NOS: 74 /FEA = mRNA /GEN = CAV2 (DNA)and 273 /PROD = caveolin 2 (amino acid) /DB_XREF = gi: 4557412 /UG =Hs.139851 caveolin 2 /FL = gb: BC005256.1 gb: AF035752.1 gb:NM_001233.1” IFNGR1: “gb: NM_000416.1 /DEF = Homo sapiens 202727_s_atsignal interferon gamma interferon gamma receptor 1 (IFNGR1),transduction receptor 1 mRNA. /FEA = mRNA /GEN = IFNGR1 (LOC3459) /PROD= interferon gamma receptor 1 SEQ ID NOS: 75 /DB_XREF = gi: 4557879(DNA) and 274 /UG = Hs.180866 interferon gamma (amino acid) receptor 1/FL = gb: BC005333.1 gb: J03143.1 gb: NM_000416.1” MGC5297: “gb:NM_024091.1 /DEF = Homo sapiens 219200_at hypothetical hypotheticalprotein MGC5297 protein MGC5297 (MGC5297), mRNA. /FEA = mRNA (LOC79072)/GEN = MGC5297 /PROD = hypothetical SEQ ID NOS: 76 protein MGC5297 (DNA)and 275 /DB_XREF = gi: 13129089 (amino acid) /UG = Hs.23856 hypotheticalprotein MGC5297 /FL = gb: BC001295.1 gb: NM_024091.1” TGFBI: “gb:NM_000358.1 /DEF = Homo sapiens 201506_at cell transforming transforminggrowth factor, beta- adhesion growth factor, induced, 68 kD (TGFBI),mRNA. beta-induced, /FEA = mRNA /GEN = TGFBI 68 kDa (LOC7045) /PROD =transforming growth factor, SEQ ID NOS: 77 beta-induced, 68 kD (DNA) and276 /DB_XREF = gi: 4507466 (amino acid) /UG = Hs.118787 transforminggrowth factor, beta-induced, 68 kD /FL = gb: BC000097.1 gb: BC004972.1gb: M77349.1 gb: NM_000358.1” AKAP2: A kinase “gb: NM_007203.1 /DEF =Homo sapiens 202760_s_at (PRKA) anchor A kinase (PRKA) anchor protein 2protein 2 (AKAP2), mRNA. /FEA = mRNA (LOC11217) /GEN = AKAP2 /PROD = Akinase SEQ ID NOS: 78 (PRKA) anchor protein 2 (DNA) and 277 /DB_XREF =gi: 6005708 /UG = Hs.42322 (amino acid) A kinase (PRKA) anchor protein 2/FL = gb: AB023137.1 gb: NM_007203.1” QKI: quaking Consensus includesgb: AI114716 212263_at signal homolog, KH /FEA = EST /DB_XREF = gi:6360061 transduction domain RNA /DB_XREF = est: HA1315 /UG = Hs.15020binding (mouse) homolog of mouse quaking QKI (KH (LOC9444) domain RNAbinding protein) SEQ ID NOS: 79 /FL = gb: AF142419.1 gb: AF142422.1(DNA) and 278 (amino acid) PRNP: prion “Consensus includes gb: AV725328215707_s_at protein (p27-30) /FEA = EST /DB_XREF = gi: 10830606(Creutzfeld-Jakob /DB_XREF = est: AV725328 disease, /CLONE = HTCAVD03/UG = Hs.74621 Gerstmann- prion protein (p27-30) (Creutzfeld-JakobStrausler- disease, Gerstmann-Strausler-Scheinker Scheinker syndrome,fatal familial insomnia)” syndrome, fatal familial insomnia) (LOC5621)SEQ ID NOS: 80 (DNA) and 279 (amino acid) HIC: I-mfa “gb: AF054589.1/DEF = Homo sapiens 211675_s_at domain-containing HIC protein isoformp40 and HIC protein protein isoform p32 mRNAs, complete cds. (LOC29969)/FEA = mRNA /PROD = HIC protein SEQ ID NOS: 81 isoform p32; HIC proteinisoform p40 (DNA) and 280 /DB_XREF = gi: 3426297 (amino acid) /FL = gb:AF054589.1” POPDC3: popeye “gb: NM_022361.1 /DEF = Homo sapiens219926_at domain containing popeye protein 3 (POP3), mRNA. 3 (LOC64208)/FEA = mRNA /GEN = POP3 SEQ ID NOS: 82 /PROD = popeye protein 3 (DNA)and 281 /DB_XREF = gi: 11641280 (amino acid) /UG = Hs.303154 popeyeprotein 3 /FL = gb: AF204171.1 gb: NM_022361.1” FLJ10315: “gb:NM_018056.1 /DEF = Homo sapiens 218770_s_at hypothetical hypotheticalprotein FLJ10315 protein FLJ10315 (FLJ10315), mRNA. /FEA = mRNA(LOC55116) /GEN = FLJ10315 /PROD = hypothetical SEQ ID NOS: 83 proteinFLJ10315 (DNA) and 282 /DB_XREF = gi: 8922347 /UG = Hs.25544 (aminoacid) hypothetical protein FLJ10315 /FL = gb: AL136695.1 gb:NM_018056.1” PSMB9: “gb: NM_002800.1 /DEF = Homo sapiens 204279_atproteolysis proteasome proteasome (prosome, macropain) and (prosome,subunit, beta type, 9 (large peptidolysis, macropain) multifunctionalprotease 2) (PSMB9), ubiquitin- subunit, beta type, mRNA. /FEA = mRNA/GEN = PSMB9 dependent 9 (large /PROD = proteasome (prosome, proteinmultifunctional macropain) subunit, betatype, 9 (large catabolismprotease 2) multifunctional protease 2) (LOC5698) /DB_XREF = gi: 4506204/UG = Hs.9280 SEQ ID NOS: 84 proteasome (prosome, macropain) (DNA) and283 subunit, beta type, 9 (large (amino acid) multifunctional protease2) /FL = gb: U01025.1 gb: NM_002800.1” DEPDC1: DEP “gb: NM_017779.1 /DEF= Homo sapiens 220295_x_at domain containing hypothetical proteinFLJ20354 1 (LOC55635) (FLJ20354), mRNA. /FEA = mRNA SEQ ID NOS: 85 /GEN= FLJ20354 /PROD = hypothetical (DNA) and 284 protein FLJ20354 (aminoacid) /DB_XREF = gi: 8923327 /UG = Hs.133260 hypothetical proteinFLJ20354 /FL = gb: NM_017779.1” EGFR: epidermal Consensus includes gb:AW157070 201983_s_at EGF growth factor /FEA = EST /DB_XREF = gi: 6228471receptor receptor /DB_XREF = est: au91e07.x1 signaling (erythroblastic/CLONE = IMAGE: 2783652 pathway leukemia viral (v- /UG = Hs.77432epidermal growth factor erb-b) oncogene receptor (avian erythroblasticleukemia homolog, avian) viral (v-erb-b) oncogene homolog) (LOC1956) /FL= gb: NM_005228.1 SEQ ID NOS: 86 (DNA) and 285 (amino acid) AMPD2:Consensus includes gb: AI916249 212360_at purine adenosine /FEA = EST/DB_XREF = gi: 5636104 nucleotide monophosphate /DB_XREF = est:wg99c01.x1 metabolism deaminase 2 /CLONE = IMAGE: 2379360 (isoform L)/UG = Hs.82927 adenosine (LOC271) monophosphate deaminase 2 (isoform L)SEQ ID NOS: 87 /FL = gb: NM_004037.2 (DNA) and 286 (amino acid) GLS:glutaminase “gb: AF158555.1 /DEF = Homo sapiens 221510_s_at glutamine(LOC2744) glutaminase C mRNA, complete cds. catabolism SEQ ID NOS: 88/FEA = mRNA /PROD = glutaminase C (DNA) and 287 /DB_XREF = gi: 5690371(amino acid) /UG = Hs.239189 glutaminase /FL = gb: AF158555.1 gb:AF097492.1” EBNA1BP2: “gb: NM_006824.1 /DEF = Homo sapiens 201323_atribosome EBNA1 binding nucleolar protein p40; homolog of yeastbiogenesis protein 2 EBNA1-binding protein (P40), mRNA. (LOC10969) /FEA= mRNA /GEN = P40 SEQ ID NOS: 89 /PROD = nucleolar protein p40; homolog(DNA) and 288 of yeastEBNA1-binding protein (amino acid) /DB_XREF = gi:5803110 /UG = Hs.74407 nucleolar protein p40; homolog of yeastEBNA1-binding protein /FL = gb: U86602.1 gb: NM_006824.1” VIM: vimentinConsensus includes gb: AI922599 201426_s_at (LOC7431) /FEA = EST/DB_XREF = gi: 5658563 SEQ ID NOS: 90 /DB_XREF = est: wm90b11.x1 (DNA)and 289 /CLONE = IMAGE: 2443197 (amino acid) /UG = Hs.297753 vimentin/FL = gb: BC000163.2 gb: NM_003380.1 ZNF258: zinc “gb: NM_007167.1 /DEF= Homo sapiens 219924_s_at development finger protein 258 zinc fingerprotein 258 (ZNF258), (LOC9204) mRNA. /FEA = mRNA /GEN = ZNF258 SEQ IDNOS: 91 /PROD = zinc finger protein 258 (DNA) and 290 /DB_XREF = gi:6005977 (amino acid) /UG = Hs.301637 zinc finger protein 258 /FL = gb:AF055470.1 gb: NM_007167.1” SGCE: “gb: NM_003919.1 /DEF = Homo sapiens204688_at muscle sarcoglycan, sarcoglycan, epsilon (SGCE), mRNA.development epsilon /FEA = mRNA /GEN = SGCE (LOC8910) /PROD =sarcoglycan, epsilon SEQ ID NOS: 92 /DB_XREF = gi: 10835046 (DNA) and291 /UG = Hs.110708 sarcoglycan, epsilon (amino acid) /FL = gb:NM_003919.1 gb: AF036364.1” CD44: CD44 “gb: M24915.1 /DEF = Human CDw44204490_s_at cell-cell antigen (homing antigen, complete cds. /FEA = mRNAadhesion function and /DB_XREF = gi: 180196 /UG = Hs.169610 Indian bloodgroup CD44 antigen (homing function and system) (LOC960) Indian bloodgroup system) SEQ ID NOS: 93 /FL = gb: NM_000610.1 gb: U40373.1 (DNA)and 292 gb: M59040.1 gb: M24915.1” (amino acid) SHCBP1: likely “gb:NM_024745.1 /DEF = Homo sapiens 219493_at ortholog of mouse hypotheticalprotein FLJ22009 Shc SH2-domain (FLJ22009), mRNA. /FEA = mRNA bindingprotein 1 /GEN = FLJ22009 /PROD = hypothetical (LOC79801) proteinFLJ22009 SEQ ID NOS: 94 /DB_XREF = gi: 13376069 (DNA) and 293 /UG =Hs.123253 hypothetical protein (amino acid) FLJ22009 /FL = gb:NM_024745.1” IMP-3: IGF-II “gb: NM_006547.1 /DEF = Homo sapiens203820_s_at protein mRNA-binding IGF-II mRNA-binding protein 3biosynthesis protein 3 (KOC1), mRNA. /FEA = mRNA (LOC10643) /GEN = KOC1/PROD = IGF-II mRNA- SEQ ID NOS: 95 binding protein 3 (DNA) and 294/DB_XREF = gi: 5729900 /UG = Hs.79440 (amino acid) IGF-II mRNA-bindingprotein 3 /FL = gb: U97188.1 gb: U76705.1 gb: AF117108.1 gb:NM_006547.1” BTG3: BTG “gb: NM_006806.1 /DEF = Homo sapiens 205548_s_atregulation family, member 3 BTG family, member 3 (BTG3), mRNA. of cell(LOC10950) /FEA = mRNA /GEN = BTG3 cycle SEQ ID NOS: 96 /PROD = BTGfamily, member 3 (DNA) and 295 /DB_XREF = gi: 5802989 /UG = Hs.77311(amino acid) BTG family, member 3 /FL = gb: D64110.1 gb: NM_006806.1”RAI14: retinoic “gb: NM_015577.1 /DEF = Homo sapiens 202052_s_at acidinduced 14 novel retinal pigment epithelial gene (LOC26064) (NORPEG),mRNA. /FEA = mRNA SEQ ID NOS: 97 /GEN = NORPEG (DNA) and 296 /PROD =DKFZP564G013 protein (amino acid) /DB_XREF = gi: 13470085 /UG = Hs.15165novel retinal pigment epithelial gene /FL = gb: NM_015577.1 gb:AF155135.1” QKI: quaking Consensus includes gb: AA149639 212262_atsignal homolog, KH /FEA = EST /DB_XREF = gi: 1720440 transduction domainRNA /DB_XREF = est: zl39c06.s1 binding (mouse) /CLONE = IMAGE: 504298(LOC9444) /UG = Hs.15020 homolog of mouse SEQ ID NOS: 98 quaking QKI (KHdomain RNA binding (DNA) and 297 protein) /FL = gb: AF142419.1 (aminoacid) gb: AF142422.1 CGI-100: CGI-100 “Consensus includes gb: AL117354202194_at intracellular protein /DEF = Human DNA sequence from cloneprotein (LOC50999) RP5-976O13 on chromosome 1p21.2-22.2 transport SEQ IDNOS: 99 Contains part of the gene for CGI- (DNA) and 298 100 protein, 3isoforms of the gene for (amino acid) M96 protein, ESTs, STSs, GSSs anda CpG Island /FEA = mRNA_1 /DB_XREF = gi: 6822199 /UG = Hs.296155CGI-100 protein /FL = gb: AF151858.1 gb: NM_016040.1” CTSZ: cathepsin Z“gb: AF073890.1 /DEF = Homo sapiens 210042_s_at proteolysis (LOC1522)cathepsin X precursor, mRNA, complete and SEQ ID NOS: 100 cds. /FEA =mRNA /PROD = cathepsin X peptidolysis (DNA) and 299 precursor /DB_XREF =gi: 3650497 (amino acid) /UG = Hs.252549 cathepsin Z /FL = gb:AF032906.1 gb: AF073890.1 gb: NM_001336.1 gb: AF136273.1”

The biomarkers provided in Table 2 include the nucleotide sequences ofSEQ ID NOS:101-200 and the amino acid sequences of SEQ ID NOS:300-395.

TABLE 2 BIOMARKERS (RESISTANT) Affymetrix Unigene title and Probe GeneSEQ ID NO: Affymetrix Description Set Ontology GATA3: GATA “gb:BC003070.1 /DEF = Homo sapiens, 209604_s_at proteolysis binding protein3 GATA-binding protein 3, clone and (LOC2625) MGC: 2346, mRNA, completecds. peptidolysis SEQ ID NOS: 101 /FEA = mRNA /PROD = GATA-binding (DNA)and 300 protein 3 /DB_XREF = gi: 13111765 (amino acid) /UG = Hs.169946GATA-binding protein 3 /FL = gb: BC003070.1 gb: M69106.1 gb:NM_002051.1” TFF1: trefoil “gb: NM_003225.1 /DEF = Homo sapiens205009_at carbohydrate factor 1 (breast trefoil factor 1 (breast cancer,estrogen- metabolism, cancer, estrogen- inducible sequence expressed in)(TFF1), cell inducible sequence mRNA. /FEA = mRNA /GEN = TFF1 growthexpressed in) /PROD = trefoil factor 1 (breast and/or (LOC7031) cancer,estrogen-inducible sequence maintenance SEQ ID NOS: 102 expressed in)/DB_XREF = gi: 4507450 (DNA) and 301 /UG = Hs.1406 trefoil factor 1(breast (amino acid) cancer, estrogen-inducible sequence expressed in)/FL = gb: NM_003225.1” ZFYVE21: zinc “gb: NM_024071.1 /DEF = Homosapiens 219929_s_at finger, FYVE hypothetical protein MGC2550 domaincontaining (MGC2550), mRNA. /FEA = mRNA 21 (LOC79038) /GEN = MGC2550/PROD = hypothetical SEQ ID NOS: 103 protein MGC2550 (DNA) and 302/DB_XREF = gi: 13129053 (amino acid) /UG = Hs.318498 hypotheticalprotein MGC2550 /FL = gb: BC001130.1 gb: NM_024071.1” ATP5G2: ATP “gb:D13119.1 /DEF = Homo sapiens P2 208764_s_at proton synthase, H+ mRNA forATP synthase subunit c, transport transporting, complete cds. /FEA =mRNA /GEN = P2 mitochondrial F0 /PROD = ATP synthase subunit c complex,subunit c precursor /DB_XREF = gi: 285909 (subunit 9), /UG = Hs.89399ATP synthase, H+ isoform 2 transporting, mitochondrial F0 complex,(LOC517) subunit c (subunit 9), isoform 2 SEQ ID NOS: 104 /FL = gb:D13119.1” (DNA) and 303 (amino acid) EGFL5: EGF-like- “Consensusincludes gb: W68084 212830_at metabolism domain, multiple 5 /FEA = EST/DB_XREF = gi: 1376954 (LOC1955) /DB_XREF = est: zd42f12.s1 SEQ ID NOS:105 /CLONE = IMAGE: 343343 /UG = Hs.5599 (DNA) and 304 EGF-like-domain,multiple 5” (amino acid) MCCC2: “gb: AB050049.1 /DEF = Homo sapiens209624_s_at leucine methylcrotonoyl- mccb mRNA for non-biotin containingcatabolism Coenzyme A subunit of 3-methylcrotonyl-CoA carboxylase 2carboxylase, complete cds. (beta) /FEA = mRNA /GEN = mccb /PROD = non-(LOC64087) biotin containing subunit of3- SEQ ID NOS: 106methylcrotonyl-CoA carboxylase (DNA) and 305 /DB_XREF = gi: 10934058(amino acid) /UG = Hs.167531 methylcrotonoyl- Coenzyme A carboxylase 2(beta) /FL = gb: AB050049.1 gb: AF310971.1 gb: AF301000.1 gb:NM_022132.2” ABAT: 4- “gb: AF237813.1 /DEF = Homo sapiens 209460_ataminobutyrate NPD009 mRNA, complete cds. aminotransferase /FEA = mRNA/PROD = NPD009 (LOC18) /DB_XREF = gi: 9963907 SEQ ID NOS: 107 /UG =Hs.283675 NPD009 protein (DNA) and 306 /FL = gb: NM_020686.1 gb:AF237813.1” (amino acid) —: Clone “Consensus includes gb: AV700224208774_at signal IMAGE: 3869896, /FEA = EST /DB_XREF = gi: 10302195transduction mRNA /DB_XREF = est: AV700224 (LOC388434) /CLONE = GKCARG01/UG = Hs.75852 SEQ ID NOS: 108 casein kinase 1, delta (DNA) /FL = gb:BC003558.1” FEM1B: fem-1 Consensus includes gb: AI799061 212367_atinduction homolog b (C. elegans) /FEA = EST /DB_XREF = gi: 5364533 of(LOC10116) /DB_XREF = est: we98a10.x1 apoptosis SEQ ID NOS: 109 /CLONE =IMAGE: 2349114 (DNA) and 307 /UG = Hs.6048 FEM-1 (C. elegans) (aminoacid) homolog b /FL = gb: AF178632.1 gb: NM_015322.1 gb: AF204883.1SLC35A1: solute “gb: NM_006416.1 /DEF = Homo sapiens 203306_s_at carrierfamily 35 solute carrier family 35 (CMP-sialic acid (CMP-sialic acidtransporter), member 1 (SLC35A1), transporter), mRNA. /FEA = mRNA /GEN =SLC35A1 member A1 /PROD = solute carrier family 35 (CMP- (LOC10559)sialic acidtransporter), member 1 SEQ ID NOS: 110 /DB_XREF = gi: 5453620/UG = Hs.82921 (DNA) and 308 solute carrier family 35 (CMP-sialic acid(amino acid) transporter), member 1 /FL = gb: D87969.1 gb: NM_006416.1”ZNF607: zinc Consensus includes gb: AL560017 200658_s_at DNA fingerprotein 607 /FEA = EST /DB_XREF = gi: 12906073 metabolism (LOC84775)/DB_XREF = est: AL560017 SEQ ID NOS: 111 /CLONE = CS0DG004YD08 (5 prime)(DNA) and 309 /UG = Hs.75323 prohibitin (amino acid) /FL = gb:NM_002634.2 FLJ11164: “gb: NM_018346.1 /DEF = Homo sapiens 218307_athypothetical hypothetical protein FLJ11164 protein FLJ11164 (FLJ11164),mRNA. /FEA = mRNA (LOC55316) /GEN = FLJ11164 /PROD = hypothetical SEQ IDNOS: 112 protein FLJ11164 (DNA) and 310 /DB_XREF = gi: 8922910 /UG =Hs.8033 (amino acid) hypothetical protein FLJ11164 /FL = gb:NM_018346.1” ABAT: 4- “gb: NM_000663.1 /DEF = Homo sapiens 206527_ataminobutyrate aminobutyrate 4-aminobutyrate aminotransferase metabolismaminotransferase (ABAT), nuclear gene encoding (LOC18) mitochondrialprotein, mRNA. SEQ ID NOS: 113 /FEA = mRNA /GEN = ABAT /PROD = 4- (DNA)and 311 aminobutyrate aminotransferase (amino acid) precursor /DB_XREF =gi: 4501846 /UG = Hs.1588 4-aminobutyrate aminotransferase /FL = gb:NM_000663.1 gb: L32961.1” SLC19A2: solute “gb: AF153330.1 /DEF = Homosapiens 209681_at small carrier family 19 thiamine carrier 1 (TC1) mRNA,molecule (thiamine complete cds. /FEA = mRNA /GEN = TC1 transporttransporter), /PROD = thiamine carrier 1 member 2 /DB_XREF = gi: 5453325/UG = Hs.30246 (LOC10560) solute carrier family 19 (thiamine SEQ ID NOS:114 transporter), member 2 (DNA) and 312 /FL = gb: AF153330.1 gb:AF135488.1 (amino acid) gb: AF160812.1” SLC9A3R1: solute “gb:NM_004252.1 /DEF = Homo sapiens 201349_at intracellular carrier family 9solute carrier family 9 (sodiumhydrogen signaling (sodium/hydrogenexchanger), isoform 3 regulatory factor 1 cascade exchanger),(SLC9A3R1), mRNA. /FEA = mRNA isoform 3 regulator /GEN = SLC9A3R1 /PROD= solute carrier 1 (LOC9368) family 9 (sodiumhydrogenexchanger), SEQ IDNOS: 115 isoform 3 regulatory factor 1 (DNA) and 313 /DB_XREF = gi:4759139 (amino acid) /UG = Hs.184276 solute carrier family 9(sodiumhydrogen exchanger), isoform 3 regulatory factor 1 /FL = gb:BC001443.1 gb: BC003361.1 gb: AF036241.1 gb: AF015926.1 gb: NM_004252.1”ICA1: islet cell “gb: L21181.1 /DEF = Human autoantigen 210547_x_atautoantigen 1, p69 mRNA, complete cds. /FEA = mRNA 69 kDa (LOC3382)/PROD = autoantigen p69 SEQ ID NOS: 116 /DB_XREF = gi: 437366 /UG =Hs.167927 (DNA) and 314 islet cell autoantigen 1 (69 kD) (amino acid)/FL = gb: L21181.1” CIRBP: cold “gb: NM_001280.1 /DEF = Homo sapiens200811_at response inducible RNA cold inducible RNA-binding protein tocold binding protein (CIRBP), mRNA. /FEA = mRNA (LOC1153) /GEN = CIRBP/PROD = cold inducible SEQ ID NOS: 117 RNA-binding protein (DNA) and 315/DB_XREF = gi: 4502846 (amino acid) /UG = Hs.119475 cold inducible RNA-binding protein /FL = gb: D78134.1 gb: BC000403.1 gb: BC000901.1 gb:AF021336.1 gb: NM_001280.1” C14orf114: “gb: NM_018199.1 /DEF = Homosapiens 218363_at chromosome 14 hypothetical protein FLJ10738 openreading (FLJ10738), mRNA. /FEA = mRNA frame 114 /GEN = FLJ10738 /PROD =hypothetical (LOC55218) protein FLJ10738 SEQ ID NOS: 118 /DB_XREF = gi:8922630 /UG = Hs.5457 (DNA) and 316 hypothetical protein FLJ10738 (aminoacid) /FL = gb: BC001962.1 gb: NM_018199.1” GREB1: GREB1 “gb:NM_014668.1 /DEF = Homo sapiens 205862_at protein KIAA0575 gene product(KIAA0575), (LOC9687) mRNA. /FEA = mRNA /GEN = KIAA0575 SEQ ID NOS: 119/PROD = KIAA0575 gene product (DNA) and 317 /DB_XREF = gi: 7662187(amino acid) /UG = Hs.193914 KIAA0575 gene product /FL = gb: AB011147.1gb: NM_014668.1” ESR1: estrogen “gb: NM_000125.1 /DEF = Homo sapiens205225_at nuclear receptor 1 estrogen receptor 1 (ESR1), mRNA. hormone(LOC2099) /FEA = mRNA /GEN = ESR1 receptor, SEQ ID NOS: 120 /PROD =estrogen receptor 1 cellular (DNA) and 318 /DB_XREF = gi: 4503602 /UG =Hs.1657 proliferation (amino acid) estrogen receptor 1 and /FL = gb:NM_000125.1” differentiation ABAT: 4- “gb: AF237813.1 /DEF = Homosapiens 209459_s_at aminobutyrate NPD009 mRNA, complete cds.aminotransferase /FEA = mRNA /PROD = NPD009 (LOC18) /DB_XREF = gi:9963907 SEQ ID NOS: 121 /UG = Hs.283675 NPD009 protein (DNA) and 319 /FL= gb: NM_020686.1 gb: AF237813.1” (amino acid) ABCG1: ATP- “gb:NM_004915.2 /DEF = Homo sapiens 204567_s_at small binding cassette,ATP-binding cassette, sub-family G molecule sub-family G (WHITE), member1 (ABCG1), transport (WHITE), member transcript variant 1, mRNA. 1(LOC9619) /FEA = mRNA /GEN = ABCG1 SEQ ID NOS: 122 /PROD = ATP-bindingcassette sub- (DNA) and 320 family G member 1isoform a (amino acid)/DB_XREF = gi: 8051574 /UG = Hs.10237 ATP-binding cassette, sub-family G(WHITE), member 1 /FL = gb: NM_004915.2” SLC35B1: solute “gb:NM_005827.1 /DEF = Homo sapiens 202433_at transport carrier family 35,UDP-galactose transporter related member B1 (UGTREL1), mRNA. /FEA = mRNA(LOC10237) /GEN = UGTREL1 /PROD = UDP- SEQ ID NOS: 123 galactosetransporter related (DNA) and 321 /DB_XREF = gi: 5032212 (amino acid)/UG = Hs.154073 UDP-galactose transporter related /FL = gb: D87989.1 gb:NM_005827.1” TOB1: transducer “Consensus includes gb: AA675892 202704_atnegative of ERBB2, 1 /FEA = EST /DB_XREF = gi: 2775239 regulation(LOC10140) /DB_XREF = est: b03503s of cell SEQ ID NOS: 124 /CLONE =b03503 /UG = Hs.178137 proliferation (DNA) and 322 transducer of ERBB2,1 (amino acid) /FL = gb: D38305.1 gb: NM_005749.1” FOXA1: forkhead “gb:NM_004496.1 /DEF = Homo sapiens 204667_at regulation box A1 hepatocytenuclear factor 3, alpha of (LOC3169) (HNF3A), mRNA. /FEA = mRNAtranscription, SEQ ID NOS: 125 /GEN = HNF3A /PROD = hepatocyte DNA-(DNA) and 323 nuclear factor 3, alpha dependent (amino acid) /DB_XREF =gi: 4758533 /UG = Hs.299867 hepatocyte nuclear factor 3, alpha /FL = gb:U39840.1 gb: NM_004496.1” LARGE: like- “Consensus includes gb:AB011181.2 215543_s_at muscle glycosyltransferase /DEF = Homo sapiensmRNA for maintenance, (LOC9215) KIAA0609 protein, partial cds.glycosphingolipid SEQ ID NOS: 126 /FEA = mRNA /GEN = KIAA0609biosynthesis (DNA) and 324 /PROD = KIAA0609 protein (amino acid)/DB_XREF = gi: 6683718 /UG = Hs.25220 like-glycosyltransferase” AKT1:v-akt “gb: NM_005163.1 /DEF = Homo sapiens 207163_s_at signal murinethymoma v-akt murine thymoma viral oncogene transduction viral oncogenehomolog 1 (AKT1), mRNA. homolog 1 /FEA = mRNA /GEN = AKT1 (LOC207) /PROD= serinethreonine protein kinase SEQ ID NOS: 127 /DB_XREF = gi: 4885060/UG = Hs.71816 (DNA) and 325 v-akt murine thymoma viral oncogene (aminoacid) homolog 1 /FL = gb: M63167.1 gb: NM_005163.1” CTPS2: CTP “gb:NM_019857.1 /DEF = Homo sapiens 219080_s_at synthase II CTP synthase II(CTPS2), mRNA. (LOC56474) /FEA = mRNA /GEN = CTPS2 SEQ ID NOS: 128 /PROD= CTP synthase II (DNA) and 326 /DB_XREF = gi: 9789918 /UG = Hs.58553(amino acid) CTP synthase II /FL = gb: AF226667.1 gb: NM_019857.1”RBM8A: RNA Consensus includes gb: AI738479 214113_s_at nuclear bindingmotif /FEA = EST /DB_XREF = gi: 5100460 mRNA protein 8A /DB_XREF = est:wi32d06.x1 splicing, (LOC9939) /CLONE = IMAGE: 2391947 via SEQ ID NOS:129 /UG = Hs.65648 RNA binding motif spliceosome (DNA) and 327 protein8A (amino acid) SIAH2: seven in “gb: U76248.1 /DEF = Human hSIAH2209339_at small absentia homolog mRNA, complete cds. /FEA = mRNA GTPase2 (Drosophila) /PROD = hSIAH2 mediated (LOC6478) /DB_XREF = gi: 2673967/UG = Hs.20191 signal SEQ ID NOS: 130 seven in absentia (Drosophila)homolog transduction (DNA) and 328 2 /FL = gb: U76248.1 gb: NM_005067.1”(amino acid) FLJ13855: “gb: NM_023079.1 /DEF = Homo sapiens 217750_s_atubiquitin hypothetical hypothetical protein FLJ13855 cycle proteinFLJ13855 (FLJ13855), mRNA. /FEA = mRNA (LOC65264) /GEN = FLJ13855 /PROD= hypothetical SEQ ID NOS: 131 protein FLJ13855 (DNA) and 329 /DB_XREF =gi: 12751494 (amino acid) /UG = Hs.168232 hypothetical protein FLJ13855/FL = gb: NM_023079.1” ITPK1: inositol “gb: AF279372.1 /DEF = Homosapiens 210740_s_at signal 1,3,4-triphosphate inositol1,3,4-trisphosphate 56-kinase transduction 5/6 kinase mRNA, completecds. /FEA = mRNA (LOC3705) /PROD = inositol 1,3,4-trisphosphate 56- SEQID NOS: 132 kinase /DB_XREF = gi: 12006345 (DNA) and 330 /UG = Hs.6453inositol 1,3,4-triphosphate (amino acid) 56 kinase /FL = gb: AF279372.1”SEPX1: “gb: NM_016332.1 /DEF = Homo sapiens 217977_at selenoprotein X, 1selenoprotein X, 1 (SEPX1), mRNA. (LOC51734) /FEA = mRNA /GEN = SEPX1SEQ ID NOS: 133 /PROD = selenoprotein X, 1 (DNA) and 331 /DB_XREF = gi:7706510 (amino acid) /UG = Hs.279623 selenoprotein X, 1 /FL = gb:AF187272.1 gb: BC003127.1 gb: AF166124.1 gb: NM_016332.1” IRX5: iroquois“gb: U90304.1 /DEF = Human iroquois- 210239_at regulation homeoboxprotein class homeodomain protein IRX-2a of 5 (LOC10265) mRNA, completecds. /FEA = mRNA transcription, SEQ ID NOS: 134 /PROD = iroquois-classhomeodomain DNA- (DNA) and 332 protein IRX-2a /DB_XREF = gi: 1899219dependent (amino acid) /UG = Hs.25351 iroquois homeobox protein 5 /FL =gb: U90304.1 gb: NM_005853.1” PTEN: “gb: BC005821.1 /DEF = Homo sapiens,211711_s_at regulation phosphatase and phosphatase and tensin homolog ofCDK tensin homolog (mutated in multiple advanced cancers activity(mutated in 1), clone MGC: 11227, mRNA, complete multiple advanced cds./FEA = mRNA /PROD = phosphatase cancers 1) and tensin homolog (mutatedinmultiple (LOC5728) advanced cancers 1) SEQ ID NOS: 135 /DB_XREF = gi:13543309 (DNA) and 333 /FL = gb: BC005821.1” (amino acid) DP1: polyposis“gb: BC000232.1 /DEF = Homo sapiens, 208873_s_at locus protein 1 Similarto deleted in polyposis 1, clone (LOC7905) MGC: 2267, mRNA, completecds. SEQ ID NOS: 136 /FEA = mRNA /PROD = Similar to deleted (DNA) and334 in polyposis 1 /DB_XREF = gi: 12652946 (amino acid) /UG = Hs.178112DNA segment, single copy probe LNS-CAILNS-CAII (deleted in polyposis /FL= gb: BC000232.1” KIAA1002: “gb: NM_014925.1 /DEF = Homo sapiens203831_at KIAA1002 protein KIAA1002 protein (KIAA1002), mRNA. (LOC22864)/FEA = mRNA /GEN = KIAA1002 SEQ ID NOS: 137 /PROD = KIAA1002 protein(DNA) and 335 /DB_XREF = gi: 7662441 (amino acid) /UG = Hs.102483KIAA1002 protein /FL = gb: AB023219.1 gb: AF113695.1 gb: NM_014925.1”PDCD4: “Consensus includes gb: N92498 212593_s_at apoptosis programmedcell /FEA = EST /DB_XREF = gi: 1264807 death 4 (neoplastic /DB_XREF =est: zb28a04.s1 transformation /CLONE = IMAGE: 304878 inhibitor) /UG =Hs.326248 Homo sapiens cDNA: (LOC27250) FLJ22071 fis, clone HEP11691”SEQ ID NOS: 138 (DNA) and 336 (amino acid) APPBP2: amyloid Consensusincludes gb: AV681579 202629_at intracellular beta precursor /FEA = EST/DB_XREF = gi: 10283442 protein protein /DB_XREF = est: AV681579transport (cytoplasmic tail) /CLONE = GKBAFE05 /UG = Hs.84084 bindingprotein 2 amyloid beta precursor protein (LOC10513) (cytoplasmictail)-binding protein 2 SEQ ID NOS: 139 /FL = gb: AF017782.1 gb:NM_006380.1 (DNA) and 337 (amino acid) ACVR1B: activin Consensusincludes gb: AL117643.1 213198_at transmembrane A receptor, type IB /DEF= Homo sapiens mRNA; cDNA receptor (LOC91) DKFZp434M245 (from cloneprotein SEQ ID NOS: 140 DKFZp434M245). /FEA = mRNA serine/threonine(DNA) and 338 /DB_XREF = gi: 5912233 /UG = Hs.5288 kinase (amino acid)Homo sapiens mRNA; cDNA signaling DKFZp434M245 (from clone pathwayDKFZp434M245) TLE3: transducin- Consensus includes gb: AW873621212770_at regulation like enhancer of /FEA = EST /DB_XREF = gi: 8007674of split 3 (E(sp1) /DB_XREF = est: ho64d03.x1 transcription, homolog,/CLONE = IMAGE: 3042149 DNA- Drosophila) /UG = Hs.31305 KIAA1547 proteindependent (LOC7090) SEQ ID NOS: 141 (DNA) and 339 (amino acid) CIRBP:cold “gb: NM_001280.1 /DEF = Homo sapiens 200810_s_at response inducibleRNA cold inducible RNA-binding protein to cold binding protein (CIRBP),mRNA. /FEA = mRNA (LOC1153) /GEN = CIRBP /PROD = cold inducible SEQ IDNOS: 142 RNA-binding protein (DNA) and 340 /DB_XREF = gi: 4502846 (aminoacid) /UG = Hs.119475 cold inducible RNA- binding protein /FL = gb:D78134.1 gb: BC000403.1 gb: BC000901.1 gb: AF021336.1 gb: NM_001280.1”ABCA3: ATP- “gb: NM_001089.1 /DEF = Homo sapiens 204343_at drug bindingcassette, ATP-binding cassette, sub-family A resistance sub-family A(ABC1), member 3 (ABCA3), mRNA. (ABC1), member /FEA = mRNA /GEN = ABCA33 (LOC21) /PROD = ATP-binding cassette, sub- SEQ ID NOS: 143 family Amember 3 (DNA) and 341 /DB_XREF = gi: 4501848 /UG = Hs.26630 (aminoacid) ATP-binding cassette, sub-family A (ABC1), member 3 /FL = gb:U78735.1 gb: NM_001089.1” MTSS1: “gb: NM_014751.1 /DEF = Homo sapiens203037_s_at metastasis KIAA0429 gene product (KIAA0429), suppressor 1mRNA. /FEA = mRNA /GEN = KIAA0429 (LOC9788) /PROD = KIAA0429 geneproduct SEQ ID NOS: 144 /DB_XREF = gi: 7662113 /UG = Hs.77694 (DNA) and342 KIAA0429 gene product (amino acid) /FL = gb: AB007889.1 gb:NM_014751.1” CA12: carbonic “gb: NM_001218.2 /DEF = Homo sapiens203963_at one- anhydrase XII carbonic anhydrase XII (CA12), mRNA. carbon(LOC771) /FEA = mRNA /GEN = CA12 compound SEQ ID NOS: 145 /PROD =carbonic anhydrase XII metabolism (DNA) and 343 precursor /DB_XREF = gi:9951924 (amino acid) /UG = Hs.5338 carbonic anhydrase XII /FL = gb:AF037335.1 gb: AF051882.1 gb: NM_001218.2” FRAT2: frequently “gb:AB045118.1 /DEF = Homo sapiens 209864_at rearranged in FRAT2 mRNA,complete cds. advanced T-cell /FEA = mRNA /GEN = FRAT2 lymphomas 2 /PROD= FRAT2 (LOC23401) /DB_XREF = gi: 13365650 SEQ ID NOS: 146 /UG =Hs.140720 GSK-3 binding protein (DNA) and 344 FRAT2 /FL = gb:AB045118.1” (amino acid) SUPT4H1: “gb: NM_003168.1 /DEF = Homo sapiens201484_at chromatin suppressor of Ty 4 suppressor of Ty (S. cerevisiae)4 modeling homolog 1 (S. cerevisiae) homolog 1 (SUPT4H1), mRNA.(LOC6827) /FEA = mRNA /GEN = SUPT4H1 SEQ ID NOS: 147 /PROD = suppressorof Ty (S. cerevisiae) 4 (DNA) and 345 homolog 1 /DB_XREF = gi: 4507310(amino acid) /UG = Hs.79058 suppressor of Ty (S. cerevisiae) 4 homolog 1/FL = gb: BC002802.1 gb: U43923.1 gb: U38818.1 gb: U38817.1 gb:NM_003168.1” UBPH: similar to “gb: NM_019116.1 /DEF = Homo sapiens205687_at ubiquitin binding similar to ubiquitin binding protein protein(UBPH), mRNA. /FEA = mRNA (LOC56061) /GEN = UBPH /PROD = similar to SEQID NOS: 148 ubiquitin binding protein (DNA) and 346 /DB_XREF = gi:9507222 (amino acid) /UG = Hs.288620 similar to ubiquitin bindingprotein /FL = gb: NM_019116.1” MGC50853: “Consensus includes gb:AL043266 212400_at hypothetical /FEA = EST /DB_XREF = gi: 5935844protein /DB_XREF = est: DKFZp434L1423_s1 MGC50853 /CLONE = DKFZp434L1423(LOC399665) /UG = Hs.111334 ferritin, light SEQ ID NOS: 149 polypeptide”(DNA) and 347 (amino acid) TBL1X: Consensus includes gb: AV753028213400_s_at signal transducin (beta)- /FEA = EST /DB_XREF = gi: 10910876transduction like 1X-linked /DB_XREF = est: AV753028 (LOC6907) /CLONE =NPDBCD07 /UG = Hs.76536 SEQ ID NOS: 150 transducin (beta)-like 1 (DNA)and 348 (amino acid) FLJ11280: Consensus includes gb: AL561943221856_s_at hypothetical /FEA = EST /DB_XREF = gi: 12909874 proteinFLJ11280 /DB_XREF = est: AL561943 (LOC55793) /CLONE = CS0DB002YO04 (3prime) SEQ ID NOS: 151 /UG = Hs.3346 hypothetical protein (DNA) and 349FLJ11280 (amino acid) RHOB: ras “Consensus includes gb: AI263909212099_at Rho homolog gene /FEA = EST /DB_XREF = gi: 3872112 proteinfamily, member B /DB_XREF = est: qi08f09.x1 signal (LOC388) /CLONE =IMAGE: 1855913 transduction SEQ ID NOS: 152 /UG = Hs.204354 ras homologgene (DNA) and 350 family, member B (amino acid) /FL = gb: NM_004040.1”LASS6: LAG1 “Consensus includes gb: BG289001 212442_s_at longevity /FEA= EST /DB_XREF = gi: 13044404 assurance homolog /DB_XREF = est:602381262F1 6 (S. cerevisiae) /CLONE = IMAGE: 4499078 (LOC253782) /UG =Hs.101282 Homo sapiens cDNA: SEQ ID NOS: 153 FLJ21238 fis, cloneCOL01115” (DNA) and 351 (amino acid) KIAA0515: “Consensus includes gb:AB011087.1 212068_s_at KIAA0515 /DEF = Homo sapiens mRNA for (LOC84726)KIAA0515 protein, partial cds. SEQ ID NOS: 154 /FEA = mRNA /GEN =KIAA0515 (DNA) /PROD = KIAA0515 protein /DB_XREF = gi: 3043553 /UG =Hs.108945 KIAA0515 protein” MCCC2: Consensus includes gb: AW439494209623_at methylcrotonoyl- /FEA = EST /DB_XREF = gi: 6974800 Coenzyme A/DB_XREF = est: xt19c01.x1 carboxylase 2 /CLONE = IMAGE: 2779584 (beta)/UG = Hs.167531 methylcrotonoyl- (LOC64087) Coenzyme A carboxylase 2(beta) SEQ ID NOS: 155 /FL = gb: AB050049.1 gb: AF310971.1 (DNA) and 352gb: AF301000.1 gb: NM_022132.2 (amino acid) TFF3: trefoil “gb:NM_003226.1 /DEF = Homo sapiens 204623_at phosphoenolpyruvate- factor 3(intestinal) trefoil factor 3 (intestinal) (TFF3), dependent (LOC7033)mRNA. /FEA = mRNA /GEN = TFF3 sugar SEQ ID NOS: 156 /PROD = trefoilfactor 3 (intestinal) phosphotransferase (DNA) and 353 /DB_XREF = gi:4507452 /UG = Hs.82961 system (amino acid) trefoil factor 3 (intestinal)/FL = gb: L08044.1 gb: L15203.1 gb: NM_003226.1” GATA3: GATA Consensusincludes gb: AI796169 209603_at defense binding protein 3 /FEA = EST/DB_XREF = gi: 5361632 response (LOC2625) /DB_XREF = est: wh43d10.x1 SEQID NOS: 157 /CLONE = IMAGE: 2383507 (DNA) and 354 /UG = Hs.169946GATA-binding protein (amino acid) 3 /FL = gb: BC003070.1 gb: M69106.1gb: NM_002051.1 CEBPA: “gb: NM_004364.1 /DEF = Homo sapiens 204039_atCCAAT/enhancer CCAATenhancer binding protein binding protein (CEBP),alpha (CEBPA), mRNA. (C/EBP), alpha /FEA = mRNA /GEN = CEBPA (LOC1050)/PROD = CCAATenhancer binding SEQ ID NOS: 158 protein (CEBP), alpha(DNA) and 355 /DB_XREF = gi: 4757971 /UG = Hs.76171 (amino acid)CCAATenhancer binding protein (CEBP), alpha /FL = gb: NM_004364.1”LOC92482: “Consensus includes gb: AK025724.1 213224_s_at hypothetical/DEF = Homo sapiens cDNA: FLJ22071 protein LOC92482 fis, clone HEP11691./FEA = mRNA (LOC92482) /DB_XREF = gi: 10438333 SEQ ID NOS: 159 /UG =Hs.326248 Homo sapiens cDNA: (DNA) FLJ22071 fis, clone HEP11691”FLJ13910: Consensus includes gb: BF671894 212482_at hypothetical /FEA =EST /DB_XREF = gi: 11945789 protein FLJ13910 /DB_XREF = est: 602151796F1(LOC64795) /CLONE = IMAGE: 4292999 SEQ ID NOS: 160 /UG = Hs.75277hypothetical protein (DNA) and 356 FLJ13910 (amino acid) C14orf130: “gb:NM_018108.1 /DEF = Homo sapiens 218108_at chromosome 14 hypotheticalprotein FLJ10483 open reading (FLJ10483), mRNA. /FEA = mRNA frame 130/GEN = FLJ10483 /PROD = hypothetical (LOC55148) protein FLJ10483 SEQ IDNOS: 161 /DB_XREF = gi: 8922451 /UG = Hs.6877 (DNA) and 357 hypotheticalprotein FLJ10483 (amino acid) /FL = gb: NM_018108.1” CDKN1B: cyclin-“gb: BC001971.1 /DEF = Homo sapiens, 209112_at regulation dependentkinase Similar to cyclin-dependent kinase of CDK inhibitor 1B (p27,inhibitor 1B (p27, Kip1), clone activity Kip1) (LOC1027) MGC: 5304,mRNA, complete cds. SEQ ID NOS: 162 /FEA = mRNA /PROD = Similar tocyclin- (DNA) and 358 dependent kinase inhibitor 1B (p27, Kip1) (aminoacid) /DB_XREF = gi: 12805034 /UG = Hs.238990 cyclin-dependent kinaseinhibitor 1B (p27, Kip1) /FL = gb: BC001971.1 gb: NM_004064.1 gb:U10906.1 gb: AF247551.1 gb: AY004255.1” APPBP2: amyloid “gb: NM_006380.1/DEF = Homo sapiens 202631_s_at intracellular beta precursor amyloidbeta precursor protein protein protein (cytoplasmic tail)-bindingprotein 2 transport (cytoplasmic tail) (APPBP2), mRNA. /FEA = mRNAbinding protein 2 /GEN = APPBP2 /PROD = amyloid beta (LOC10513)precursor protein (cytoplasmictail)- SEQ ID NOS: 163 binding protein 2(DNA) and 359 /DB_XREF = gi: 5453552 /UG = Hs.84084 (amino acid) amyloidbeta precursor protein (cytoplasmic tail)-binding protein 2 /FL = gb:AF017782.1 gb: NM_006380.1” LOC81558: “gb: NM_030802.1 /DEF = Homosapiens 221249_s_at C/EBP-induced CEBP-induced protein (LOC81558),protein mRNA. /FEA = mRNA /GEN = LOC81558 (LOC81558) /PROD =CEBP-induced protein SEQ ID NOS: 164 /DB_XREF = gi: 13540589 (DNA) and360 /FL = gb: NM_030802.1” (amino acid) FLJ20274: Consensus includes gb:AL134904 213025_at hypothetical /FEA = EST /DB_XREF = gi: 6603091protein FLJ20274 /DB_XREF = est: DKFZp762M0710_s1 (LOC55623) /CLONE =DKFZp762M0710 SEQ ID NOS: 165 /UG = Hs.268371 hypothetical protein (DNA)and 361 FLJ20274 (amino acid) RAB11A: “gb: NM_004663.1 /DEF = Homosapiens 200864_s_at intracellular RAB11A, member RAB11A, member RASoncogene family protein RAS oncogene (RAB11A), mRNA. /FEA = mRNAtransport family (LOC8766) /GEN = RAB11A /PROD = RAB11A, SEQ ID NOS: 166member RAS oncogene family (DNA) and 362 /DB_XREF = gi: 4758983 /UG =Hs.75618 (amino acid) RAB11A, member RAS oncogene family /FL = gb:AF000231.1 gb: NM_004663.1” —: MRNA; cDNA Consensus includes gb:BE967207 212114_at DKFZp313P052 /FEA = EST /DB_XREF = gi: 11773627 (fromclone /DB_XREF = est: 601661094R1 DKFZp313P052) /CLONE = IMAGE: 3916174(LOC387869) /UG = Hs.165590 ribosomal protein S13 SEQ ID NOS: 167 (DNA)and 363 (amino acid) NPEPPS: “Consensus includes gb: AJ132583.1201455_s_at proteolysis aminopeptidase /DEF = Homo sapiens mRNA for andpuromycin puromycin sensitive aminopeptidase, peptidolysis sensitivepartial. /FEA = mRNA (LOC9520) /PROD = puromycin sensitive SEQ ID NOS:168 aminopeptidase /DB_XREF = gi: 4210725 (DNA) and 364 /UG = Hs.293007aminopeptidase (amino acid) puromycin sensitive /FL = gb: NM_006310.1”UBL3: ubiquitin- “gb: AF044221.1 /DEF = Homo sapiens 201534_s_at like 3(LOC5412) HCG-1 protein (HCG-1) mRNA, SEQ ID NOS: 169 complete cds. /FEA= mRNA (DNA) and 365 /GEN = HCG-1 /PROD = HCG-1 protein (amino acid)/DB_XREF = gi: 4105251 /UG = Hs.173091 ubiquitin-like 3 /FL = gb:AF044221.1 gb: AL080177.1 gb: NM_007106.1” BAMBI: BMP and “gb:NM_012342.1 /DEF = Homo sapiens 203304_at activin membrane- putativetransmembrane protein (NMA), bound inhibitor mRNA. /FEA = mRNA /GEN =NMA homolog (Xenopus /PROD = putative transmembrane protein laevis)/DB_XREF = gi: 6912533 /UG = Hs.78776 (LOC25805) putative transmembraneprotein SEQ ID NOS: 170 /FL = gb: U23070.1 gb: NM_012342.1” (DNA) and366 (amino acid) GABPB2: GA “gb: NM_005254.2 /DEF = Homo sapiens204618_s_at regulation binding protein GA-binding protein transcriptionfactor, of transcription beta subunit 1 (53 kD) (GABPB1), transcription,factor, beta subunit transcript variant beta, mRNA. DNA- 2, 47 kDa /FEA= mRNA /GEN = GABPB1 dependent (LOC2553) /PROD = GA-binding protein SEQID NOS: 171 transcription factor, betasubunit 1 (DNA) and 367 (53 kD),isoform beta 1 (amino acid) /DB_XREF = gi: 8051592 /UG = Hs.78915GA-binding protein transcription factor, beta subunit 1 (53 kD) /FL =gb: U13045.1 gb: NM_005254.2” MAPT: “gb: J03778.1 /DEF = Humanmicrotubule- 206401_s_at microtubule microtubule- associated protein taumRNA, complete cytoskeleton associated protein cds. /FEA = mRNA /GEN =MTBT1 organization tau (LOC4137) /DB_XREF = gi: 338684 /UG = Hs.101174and SEQ ID NOS: 172 microtubule-associated protein tau biogenesis (DNA)and 368 /FL = gb: BC000558.1 gb: J03778.1 (amino acid) gb: NM_016841.1”WBSCR21: Consensus includes gb: AI923458 221927_s_at Williams Beuren/FEA = EST /DB_XREF = gi: 5659422 syndrome /DB_XREF = est: wn85h04.x1chromosome /CLONE = IMAGE: 2452663 region 21 /UG = Hs.182476 Homosapiens clone (LOC83451) PP1226 unknown mRNA SEQ ID NOS: 173 (DNA) and369 (amino acid) ZNF278: zinc “gb: AF242522.1 /DEF = Homo sapiens211392_s_at finger protein 278 krueppel-related zinc finger protein(LOC23598) SBZF5 mRNA, complete cds. SEQ ID NOS: 174 /FEA = mRNA /PROD =krueppel-related (DNA) and 370 zinc finger protein SBZF5 (amino acid)/DB_XREF = gi: 9802041 /UG = Hs.27801 zinc finger protein 278 /FL = gb:AF242522.1” SUPT4H1: “gb: BC002802.1 /DEF = Homo sapiens, 201483_s_atchromatin suppressor of Ty 4 suppressor of Ty (S. cerevisiae) 4 modelinghomolog 1 (S. cerevisiae) homolog 1, clone MGC: 3864, mRNA, (LOC6827)complete cds. /FEA = mRNA SEQ ID NOS: 175 /PROD = suppressor of Ty (S.cerevisiae) 4 (DNA) and 371 homolog 1 /DB_XREF = gi: 12803910 (aminoacid) /UG = Hs.79058 suppressor of Ty (S. cerevisiae) 4 homolog 1 /FL =gb: BC002802.1 gb: U43923.1 gb: U38818.1 gb: U38817.1 gb: NM_003168.1”RAB4B: RAB4B, “gb: NM_016154.1 /DEF = Homo sapiens 219807_x_at memberRAS ras-related GTP-binding protein 4b oncogene family (RAB4B), mRNA./FEA = mRNA (LOC53916) /GEN = RAB4B /PROD = ras-related GTP- SEQ ID NOS:176 binding protein 4b (DNA) and 372 /DB_XREF = gi: 7706672 (amino acid)/UG = Hs.279771 Homo sapiens TR00071289_m (RAB4B), mRNA /FL = gb:AF165522.1 gb: NM_016154.1” PEX11B: “gb: NM_003846.1 /DEF = Homo sapiens202658_at peroxisome peroxisomal peroxisomal biogenesis factor 11Borganization biogenesis factor (PEX11B), mRNA. /FEA = mRNA and 11B(LOC8799) /GEN = PEX11B /PROD = peroxisomal biogenesis SEQ ID NOS: 177biogenesis factor 11B (DNA) and 373 /DB_XREF = gi: 4505718 /UG =Hs.83023 (amino acid) peroxisomal biogenesis factor 11B /FL = gb:AF093670.1 gb: AB018080.1 gb: NM_003846.1” LASS6: LAG1 “Consensusincludes gb: AI658534 212446_s_at longevity /FEA = EST /DB_XREF = gi:4762104 assurance homolog /DB_XREF = est: tu17g01.x1 6 (S. cerevisiae)/CLONE = IMAGE: 2251344 (LOC253782) /UG = Hs.101282 Homo sapiens cDNA:SEQ ID NOS: 178 FLJ21238 fis, clone COL01115” (DNA) and 374 (amino acid)C10orf86: “gb: BC005212.1 /DEF = Homo sapiens, 211376_s_at chromosome 10Similar to hypothetical protein open reading FLJ20003, clone MGC: 12228,mRNA, frame 86 complete cds. /FEA = mRNA (LOC54780) /PROD = Similar tohypothetical protein SEQ ID NOS: 179 FLJ20003 /DB_XREF = gi: 13528824(DNA) and 375 /UG = Hs.258798 hypothetical protein (amino acid) FLJ20003/FL = gb: BC005212.1” PLEKHF2: “gb: NM_024613.1 /DEF = Homo sapiens218640_s_at pleckstrin hypothetical protein FLJ13187 homology domain(FLJ13187), mRNA. /FEA = mRNA containing, family /GEN = FLJ13187 /PROD =hypothetical F (with FYVE protein FLJ13187 domain) member 2 /DB_XREF =gi: 13375826 (LOC79666) /UG = Hs.29724 hypothetical protein SEQ ID NOS:180 FLJ13187 /FL = gb: NM_024613.1” (DNA) and 376 (amino acid) KIAA0261:“Consensus includes gb: D87450.1 212267_at KIAA0261 /DEF = Human mRNAfor KIAA0261 (LOC23063) gene, partial cds. /FEA = mRNA SEQ ID NOS: 181/GEN = KIAA0261 (DNA) and 377 /DB_XREF = gi: 1665788 (amino acid) /UG =Hs.154978 KIAA0261 protein” TIP120A: TBP- gb: AL136810.1 /DEF = Homosapiens 208839_s_at interacting protein mRNA; cDNA DKFZp434G0222 (from(LOC55832) clone DKFZp434G0222); complete cds. SEQ ID NOS: 182 /FEA =mRNA /GEN = DKFZp434G0222 (DNA) and 378 /PROD = hypothetical protein(amino acid) /DB_XREF = gi: 12053130 /UG = Hs.184786 TBP-interactingprotein /FL = gb: AL136810.1 GATA3: GATA Consensus includes gb: AI796169209602_s_at defense binding protein 3 /FEA = EST /DB_XREF = gi: 5361632response (LOC2625) /DB_XREF = est: wh43d10.x1 SEQ ID NOS: 183 /CLONE =IMAGE: 2383507 (DNA) and 379 /UG = Hs.169946 GATA-binding protein (aminoacid) 3 /FL = gb: BC003070.1 gb: M69106.1 gb: NM_002051.1 CGI-85: CGI-85“gb: NM_017635.1 /DEF = Homo sapiens 218242_s_at protein hypotheticalprotein FLJ20039 (LOC51111) (FLJ20039), mRNA. /FEA = mRNA SEQ ID NOS:184 /GEN = FLJ20039 /PROD = hypothetical (DNA) and 380 protein FLJ20039(amino acid) /DB_XREF = gi: 8923045 /UG = Hs.267448 hypothetical proteinFLJ20039 /FL = gb: NM_017635.1” C20orf11: “gb: NM_017896.1 /DEF = Homosapiens 218448_at chromosome 20 hypothetical protein FLJ20602 openreading (FLJ20602), mRNA. /FEA = mRNA frame 11 /GEN = FLJ20602 /PROD =hypothetical (LOC54994) protein FLJ20602 SEQ ID NOS: 185 /DB_XREF = gi:8923556 (DNA) and 381 /UG = Hs.103808 hypothetical protein (amino acid)FLJ20602 /FL = gb: NM_017896.1” IGF1R: insulin- Consensus includes gb:H05812 203628_at signal like growth factor /FEA = EST /DB_XREF = gi:869364 transduction 1 receptor /DB_XREF = est: yl77f04.s1 (LOC3480)/CLONE = IMAGE: 44149 SEQ ID NOS: 186 /UG = Hs.239176 insulin-likegrowth (DNA) and 382 factor 1 receptor /FL = gb: NM_000875.2 (aminoacid) LOC51315: “gb: NM_016618.1 /DEF = Homo sapiens 218303_x_athypothetical hypothetical protein (LOC51315), protein LOC51315 mRNA./FEA = mRNA /GEN = LOC51315 (LOC51315) /PROD = hypothetical protein SEQID NOS: 187 /DB_XREF = gi: 7706155 /UG = Hs.5721 (DNA) and 383hypothetical protein /FL = gb: AF208845.1 (amino acid) gb: AF217520.1gb: NM_016618.1” PBP: prostatic “gb: NM_002567.1 /DEF = Homo sapiens205353_s_at binding protein prostatic binding protein (PBP), mRNA.(LOC5037) /FEA = mRNA /GEN = PBP SEQ ID NOS: 188 /PROD = prostaticbinding protein (DNA) and 384 /DB_XREF = gi: 4505620 /UG = Hs.80423(amino acid) prostatic binding protein /FL = gb: D16111.1 gb:NM_002567.1” KIAA0602: “Cluster Incl. AB011174: Homo sapiens 34406_atKIAA0602 protein mRNA for KIAA0602 protein, partial (LOC23241) cds /cds= (0,2889) /gb = AB011174 SEQ ID NOS: 189 /gi = 3043727 /ug = Hs.37656/len = 3428” (DNA) MYST2: MYST “gb: NM_007067.1 /DEF = Homo sapiens200049_at regulation histone histone acetyltransferase (HBOA), ofacetyltransferase 2 mRNA. /FEA = mRNA /GEN = HBOA transcription,(LOC11143) /PROD = histone acetyltransferase DNA- SEQ ID NOS: 190/DB_XREF = gi: 5901961 /UG = Hs.21907 dependent (DNA) and 385 histoneacetyltransferase (amino acid) /FL = gb: AF074606.1 gb: AF140360.1 gb:NM_007067.1” C6orf211: “gb: NM_024573.1 /DEF = Homo sapiens 218195_atchromosome 6 hypothetical protein FLJ12910 open reading (FLJ12910),mRNA. /FEA = mRNA frame 211 /GEN = FLJ12910 /PROD = hypothetical(LOC79624) protein FLJ12910 SEQ ID NOS: 191 /DB_XREF = gi: 13375745(DNA) and 386 /UG = Hs.15929 hypothetical protein (amino acid) FLJ12910/FL = gb: NM_024573.1” C20orf149: “gb: NM_024299.1 /DEF = Homo sapiens218010_x_at chromosome 20 hypothetical protein MGC2479 open reading(MGC2479), mRNA. /FEA = mRNA frame 149 /GEN = MGC2479 /PROD =hypothetical (LOC79144) protein MGC2479 SEQ ID NOS: 192 /DB_XREF = gi:13236523 (DNA) and 387 /UG = Hs.79625 hypothetical protein (amino acid)MGC2479 /FL = gb: BC002531.1 gb: NM_024299.1” LLGL2: lethal “gb:NM_004524.1 /DEF = Homo sapiens 203713_s_at giant larvae lethal giantlarvae (Drosophila) homolog homolog 2 2 (LLGL2), mRNA. /FEA = mRNA(Drosophila) /GEN = LLGL2 /PROD = lethal giant (LOC3993) larvae(Drosophila) homolog 2 SEQ ID NOS: 193 /DB_XREF = gi: 4758679 /UG =Hs.3123 (DNA) and 388 lethal giant larvae (Drosophila) homolog (aminoacid) 2 /FL = gb: NM_004524.1” KIAA0882: Consensus includes gb: AI348094212956_at KIAA0882 protein /FEA = EST /DB_XREF = gi: 4085300 (LOC23158)/DB_XREF = est: qp61g12.x1 SEQ ID NOS: 194 /CLONE = IMAGE: 1927558 (DNA)and 389 /UG = Hs.90419 KIAA0882 protein (amino acid) CA12: carbonic “gb:BC001012.1 /DEF = Homo sapiens, 204508_s_at anhydrase XII hypotheticalprotein FLJ20151, clone (LOC771) MGC: 1073, mRNA, complete cds. SEQ IDNOS: 195 /FEA = mRNA /PROD = hypothetical (DNA) and 390 protein FLJ20151(amino acid) /DB_XREF = gi: 12654376 /UG = Hs.279916 hypotheticalprotein FLJ20151 /FL = gb: BC001012.1 gb: NM_017689.1” SLC2A10: solute“gb: NM_030777.1 /DEF = Homo sapiens 221024_s_at glucose carrier family2 solute carrier family 2 (facilitated transport (facilitated glucoseglucose transporter), member 10 transporter), (SLC2A10), mRNA. /FEA =mRNA member 10 /GEN = SLC2A10 /PROD = solute carrier (LOC81031) family 2(facilitated glucosetransporter), SEQ ID NOS: 196 member 10 /DB_XREF =gi: 13540546 (DNA) and 391 /FL = gb: NM_030777.1” (amino acid) TRIM37:tripartite “Consensus includes gb: AK022701.1 213009_s_atmotif-containing /DEF = Homo sapiens cDNA FLJ12639 37 (LOC4591) fis,clone NT2RM4001938, highly SEQ ID NOS: 197 similar to Homo sapiens mRNAfor (DNA) and 392 KIAA0898 protein. /FEA = mRNA (amino acid) /DB_XREF =gi: 10434250 /UG = Hs.8164 Mulibrey nanism” AP1G1: adaptor- “Consensusincludes gb: AL050025.1 215867_x_at endocytosis related protein /DEF =Homo sapiens mRNA; cDNA complex 1, gamma DKFZp564D066 (from clone 1subunit DKFZp564D066); partial cds. (LOC164) /FEA = mRNA /GEN =DKFZp564D066 SEQ ID NOS: 198 /PROD = hypothetical protein (DNA) and 393/DB_XREF = gi: 4884095 /UG = Hs.5344 (amino acid) adaptor-relatedprotein complex 1, gamma 1 subunit” UBL3: ubiquitin- “gb: NM_007106.1/DEF = Homo sapiens 201535_at like 3 (LOC5412) ubiquitin-like 3 (UBL3),mRNA. SEQ ID NOS: 199 /FEA = mRNA /GEN = UBL3 (DNA) and 394 /PROD =ubiquitin-like 3 (amino acid) /DB_XREF = gi: 6005927 /UG = Hs.173091ubiquitin-like 3 /FL = gb: AF044221.1 gb: AL080177.1 gb: NM_007106.1”CYB561: “Consensus includes gb: U06715.1 217200_x_at secretorycytochrome b-561 /DEF = Human cytochrome B561, vesicle- (LOC1534) HCYTOB561, mRNA, partial cds. specific SEQ ID NOS: 200 /FEA = mRNA /GEN =B561 electron (DNA) and 395 /PROD = HCYTO B561 transport (amino acid)/DB_XREF = gi: 476590 /UG = Hs.153028 protein cytochrome b-561”

Certain biomarkers were of particular interest. Microtubule-associatedprotein tau was identified as one of the resistance markers, and hasbeen shown to bind at the close site of microtubule where Taxol® bindsto. It is believed that Taxol® interferes microtubule and Tauinteraction, but Tau's interaction seems more resistant than Taxol® (R.Dye et al., J. Biological Chem., 268, 6847-6850 (1993)). Therefore, thisfurther validates the observation that Tau expressing cells are moreresistant to ixabepilone treatment as ixabepilone binds at the same siteof Taxol® in tubulin. Another interesting resistance biomarker isestrogen receptor. In general, estrogen-receptor status is predictive ofresponse to hormonal treatments. (J. C. Chang et al., Lancet, 362,362-369 (2003)). However, it was interesting to observe estrogenreceptor as a strong marker for the resistance to ixabepilone. ER hasnot been previously suggested as a predictive marker of a patient'sresponse to chemotherapy. More interestingly, microtubule associatedprotein tau is estrogen induced (M. West et al., P. N. A. S. USA, 98,11462-11467 (2001)). ER and Tau were also found as resistance markers inan analysis of Taxol® (data not provided), and this suggests that Tauand ER both are likely to be the resistance markers formicrotubule-stabilizing agents such as ixabepilone and Taxol®.

Several other genes appear promising as potential markers includingtransporter genes (ATP-binding cassette, sub-family G (WHITE), member 1and ATP-binding cassette, sub-family A (ABC1), member 3), Midline 1 (C.Berti et al., BMC Cell Biol., February 29; 5(1):9 (2004)), LMP7 and etc.The differential expression patterns of these biomarkers were distinctbetween the two phenotypes of the cell lines (sensitive and resistant).In addition, their biological functions are involved in drug resistancemechanism or related with microtubule functions. Furthermore, theirdifferential expression patterns observed within tumors support theirpotential as response markers.

Microtubule-Stabilizing Agents

Agents that affect microtubule-stabilization are well known in the art.These agents have cytotoxic activity against rapidly proliferatingcells, such as, tumor cells or other hyperproliferative cellulardisease.

In one aspect, the microtubule-stabilizing agent is an epothilone, oranalog or derivative thereof. The epothilones, including analogs andderivatives thereof, may be found to exert microtubule-stabilizingeffects similar to paclitaxel (Taxol®) and, hence, cytotoxic activityagainst rapidly proliferating cells, such as, tumor cells or otherhyperproliferative cellular disease.

Suitable microtubule-stabilizing agents are disclosed, for example, inthe following PCT publications hereby incorporated by reference:WO93/10121; WO98/22461; WO99/02514; WO99/58534; WO00/39276; WO02/14323;WO02/72085; WO02/98868; WO03/070170; WO03/77903; WO03/78411; WO04/80458;WO04/56832; WO04/14919; WO03/92683; WO03/74053; WO03/57217; WO03/22844;WO03/103712; WO03/07924; WO02/74042; WO02/67941; WO01/81342; WO00/66589;WO00/58254; WO99/43320; WO99/42602; WO99/39694; WO99/16416; WO 99/07692;WO99/03848; WO99/01124; and WO 98/25929.

In another aspect, the microtubule-stabilizing agent is ixabepilone.Ixabepilone is a semi-synthetic analog of the natural product epothiloneB that binds to tubulin in the same binding site as paclitaxel, butinteracts with tubulin differently. (P. Giannakakou et al., P. N. A. S.USA, 97, 2904-2909 (2000)).

In another aspect, the microtubule-stabilizing agent is a taxane. Thetaxanes are well known in the art and include, for example, paclitaxel(Taxol®) and docetaxel (Taxotere®).

Biomarkers and Biomarker Sets

The invention includes individual biomarkers and biomarker sets havingboth diagnostic and prognostic value in disease areas in whichmicrotubule-stabilization and/or cytotoxic activity against rapidlyproliferating cells, such as, tumor cells or other hyperproliferativecellular disease is of importance, e.g., in cancers or tumors. Thebiomarker sets comprise a plurality of biomarkers such as, for example,a plurality of the biomarkers provided in Table 1 and Table 2, thathighly correlate with resistance or sensitivity to one or moremicrotubule-stabilizing agents.

The biomarker sets of the invention enable one to predict or reasonablyforetell the likely effect of one or more microtubule-stabilizing agentsin different biological systems or for cellular responses. The biomarkersets can be used in in vitro assays of microtubule-stabilizing agentresponse by test cells to predict in vivo outcome. In accordance withthe invention, the various biomarker sets described herein, or thecombination of these biomarker sets with other biomarkers or markers,can be used, for example, to predict how patients with cancer mightrespond to therapeutic intervention with one or moremicrotubule-stabilizing agents.

A biomarker set of cellular gene expression patterns correlating withsensitivity or resistance of cells following exposure of the cells toone or more microtubule-stabilizing agents provides a useful tool forscreening one or more tumor samples before treatment with themicrotubule-stabilizing agent. The screening allows a prediction ofcells of a tumor sample exposed to one or more microtubule-stabilizingagents, based on the expression results of the biomarker set, as towhether or not the tumor, and hence a patient harboring the tumor, willor will not respond to treatment with the microtubule-stabilizing agent.

The biomarker or biomarker set can also be used as described herein formonitoring the progress of disease treatment or therapy in thosepatients undergoing treatment for a disease involving amicrotubule-stabilizing agent.

The biomarkers also serve as targets for the development of therapiesfor disease treatment. Such targets may be particularly applicable totreatment of breast cancers or tumors. Indeed, because these biomarkersare differentially expressed in sensitive and resistant cells, theirexpression patterns are correlated with relative intrinsic sensitivityof cells to treatment with microtubule-stabilizing agents. Accordingly,the biomarkers highly expressed in resistant cells may serve as targetsfor the development of new therapies for the tumors which are resistantto microtubule-stabilizing agents.

The level of biomarker protein and/or mRNA can be determined usingmethods well known to those skilled in the art. For example,quantification of protein can be carried out using methods such asELISA, 2-dimensional SDS PAGE, Western blot, immunopreciptation,immunohistochemistry, fluorescence activated cell sorting (FACS), orflow cytometry. Quantification of mRNA can be carried out using methodssuch as PCR, array hybridization, Northern blot, in-situ hybridization,dot-blot, Taqman, or RNAse protection assay.

Microarrays

The invention also includes specialized microarrays, e.g.,oligonucleotide microarrays or cDNA microarrays, comprising one or morebiomarkers, showing expression profiles that correlate with eithersensitivity or resistance to one or more microtubule-stabilizing agents.Such microarrays can be employed in in vitro assays for assessing theexpression level of the biomarkers in the test cells from tumorbiopsies, and determining whether these test cells are likely to beresistant or sensitive to microtubule-stabilizing agents. For example, aspecialized microarray can be prepared using all the biomarkers, orsubsets thereof, as described herein and shown in Table 1 and Table 2.Cells from a tissue or organ biopsy can be isolated and exposed to oneor more of the microtubule-stabilizing agents. Following application ofnucleic acids isolated from both untreated and treated cells to one ormore of the specialized microarrays, the pattern of gene expression ofthe tested cells can be determined and compared with that of thebiomarker pattern from the control panel of cells used to create thebiomarker set on the microarray. Based upon the gene expression patternresults from the cells that underwent testing, it can be determined ifthe cells show a resistant or a sensitive profile of gene expression.Whether or not the tested cells from a tissue or organ biopsy willrespond to one or more of the microtubule-stabilizing agents and thecourse of treatment or therapy can then be determined or evaluated basedon the information gleaned from the results of the specializedmicroarray analysis.

Antibodies

The invention also includes antibodies, including polyclonal ormonoclonal, directed against one or more of the polypeptide biomarkers.Such antibodies can be used in a variety of ways, for example, topurify, detect, and target the biomarkers of the invention, includingboth in vitro and in vivo diagnostic, detection, screening, and/ortherapeutic methods.

Kits

The invention also includes kits for determining or predicting whether apatient would be susceptible or resistant to a treatment that comprisesone or more microtubule-stabilizing agents. The patient may have acancer or tumor such as, for example, a breast cancer or tumor. Suchkits would be useful in a clinical setting for use in testing apatient's biopsied tumor or other cancer samples, for example, todetermine or predict if the patient's tumor or cancer will be resistantor sensitive to a given treatment or therapy with amicrotubule-stabilizing agent. The kit comprises a suitable containerthat comprises: one or more microarrays, e.g., oligonucleotidemicroarrays or cDNA microarrays, that comprise those biomarkers thatcorrelate with resistance and sensitivity to microtubule-stabilizingagents; one or more microtubule-stabilizing agents for use in testingcells from patient tissue specimens or patient samples; and instructionsfor use. In addition, kits contemplated by the invention can furtherinclude, for example, reagents or materials for monitoring theexpression of biomarkers of the invention at the level of mRNA orprotein, using other techniques and systems practiced in the art suchas, for example, RT-PCR assays, which employ primers designed on thebasis of one or more of the biomarkers described herein, immunoassays,such as enzyme linked immunosorbent assays (ELISAs), immunoblotting,e.g., Western blots, or in situ hybridization, and the like, as furtherdescribed herein.

Application of Biomarkers and Biomarker Sets

The biomarkers and biomarker sets may be used in different applications.Biomarker sets can be built from any combination of biomarkers listed inTable 1 and Table 2 to make predictions about the likely effect of anymicrotubule-stabilizing agent in different biological systems. Thevarious biomarkers and biomarkers sets described herein can be used, forexample, as diagnostic or prognostic indicators in disease management,to predict how patients with cancer might respond to therapeuticintervention with a microtubule-stabilizing agent, and to predict howpatients might respond to therapeutic intervention that affectsmicrotubule-stabilization and/or cytotoxic activity against rapidlyproliferating cells, such as, tumor cells or other hyperproliferativecellular disease.

The biomarkers have both diagnostic and prognostic value in diseasesareas in which microtubule-stabilization and/or cytotoxic activityagainst rapidly proliferating cells, such as, tumor cells or otherhyperproliferative cellular disease is of importance.

In accordance with the invention, cells from a patient tissue sample,e.g., a tumor or cancer biopsy, can be assayed to determine theexpression pattern of one or more biomarkers prior to treatment with oneor more microtubule-stabilizing agents. In one aspect, the tumor orcancer is breast cancer. Success or failure of a treatment can bedetermined based on the biomarker expression pattern of the cells fromthe test tissue (test cells), e.g., tumor or cancer biopsy, as beingrelatively similar or different from the expression pattern of a controlset of the one or more biomarkers. Thus, if the test cells show abiomarker expression profile which corresponds to that of the biomarkersin the control panel of cells which are sensitive to themicrotubule-stabilizing agent, it is highly likely or predicted that theindividual's cancer or tumor will respond favorably to treatment withthe microtubule-stabilizing agent. By contrast, if the test cells show abiomarker expression pattern corresponding to that of the biomarkers ofthe control panel of cells which are resistant to themicrotubule-stabilizing agent, it is highly likely or predicted that theindividual's cancer or tumor will not respond to treatment with themicrotubule-stabilizing agent.

The invention also provides a method of monitoring the treatment of apatient having a disease treatable by one or moremicrotubule-stabilizing agents. The isolated test cells from thepatient's tissue sample, e.g., a tumor biopsy or tumor sample, can beassayed to determine the expression pattern of one or more biomarkersbefore and after exposure to a microtubule-stabilizing agent. Theresulting biomarker expression profile of the test cells before andafter treatment is compared with that of one or more biomarkers asdescribed and shown herein to be highly expressed in the control panelof cells that are either resistant or sensitive to amicrotubule-stabilizing agent. Thus, if a patient's response issensitive to treatment by a microtubule-stabilizing agent, based oncorrelation of the expression profile of the one or biomarkers, thepatient's treatment prognosis can be qualified as favorable andtreatment can continue. Also, if, after treatment with amicrotubule-stabilizing agent, the test cells don't show a change in thebiomarker expression profile corresponding to the control panel of cellsthat are sensitive to the microtubule-stabilizing agent, it can serve asan indicator that the current treatment should be modified, changed, oreven discontinued. This monitoring process can indicate success orfailure of a patient's treatment with a microtubule-stabilizing agentand such monitoring processes can be repeated as necessary or desired.

The biomarkers of the invention can be used to predict an outcome priorto having any knowledge about a biological system. Essentially, abiomarker can be considered to be a statistical tool. Biomarkers areuseful in predicting the phenotype that is used to classify thebiological system.

Although the complete function of all of the biomarkers are notcurrently known, some of the biomarkers are likely to be directly orindirectly involved in microtubule-stabilization and/or cytotoxicactivity against rapidly proliferating cells. In addition, some of thebiomarkers may function in metabolic or other resistance pathwaysspecific to the microtubule-stabilizing agents tested. Notwithstanding,knowledge about the function of the biomarkers is not a requisite fordetermining the accuracy of a biomarker according to the practice of theinvention.

EXAMPLES Example 1 Identification of Biomarkers Methods

Cell Lines and Cytotoxicity Assay

23 breast cancer cell lines were assayed for their sensitivity toixabepilone. Each cell line was exposed to ixabepilone for 72 hours, andgrowth inhibition was assessed by the CellTiter 96® AqueousNon-Radioactive Cell proliferation Assay (Promega) for IC₅₀measurements. Then, the concentration of the ixabepilone required for50% growth inhibition was calculated as the IC₅₀. For each experimentalcondition, at least triplicate measurements were carried out for eachcell line. The 23 cell lines were assayed for their IC₅₀ measurementstwice, and these two separate IC₅₀ data sets were used for the followinganalysis.

Training Set Selection

For analysis, training cell lines were chosen in the following manner.The 23 cell lines were assigned into the classes “sensitive” or“resistant” using IC₅₀ values; log(IC₅₀) values were normalized based onthe mean and the standard deviation (SD) across the 23 cell lines foreach IC₅₀ data set. (J. E. Staunton et al., P. N. A. S. USA. 98,10787-10792 (2001)) The cell lines with the normalized log(IC₅₀) belowthe mean of log(IC₅₀)s were classified as sensitive and above asresistant. Subsequently, classification of the cell lines were comparedin two separate experiments and 18 cell lines that exhibited consistentIC₅₀ and classification were chosen as a training set for subsequentmarker analysis. Five cell lines with inconsistent IC₅₀ andclassification were considered to be intermediate and were eliminatedfrom the analysis.

RNA Extraction and Gene Expression Data

The 23 breast cancer cell lines were grown to 50-70% confluent in RPMImedia with FBS 10% at 37° C. and 5% CO₂. RNA was isolated using theRNeasy Mini kit (Qiagen) according to the manufacturer's instructions.10 ug of total RNA was used to prepare biotinylated cRNA targets asdescribed in Affymetrix protocol. Targets were hybridized to Affymetrixhigh-density HU133 A and B set that consist of 44,000 probe setscontaining ˜32,000 genes. The chips were washed and stained usingrecommended procedures for GeneChip®. Expression values were calculatedand scaled to 1500 by using Affymetrix GeneChip® software.

k-Nearest Neighbors (KNN) Analysis

GeneCluster software was used to find a set of marker genes. First,genes with greater than 100 average difference were filtered. Then,genes were excluded if they varied by less than 2-fold and 1000 averagedifference change across 18 training cell lines. Subsequently, intensityunits across the cell lines for each gene were normalized to the meanand variance. The genes were ranked according to the correlation betweentheir expression level, and the sensitivity and resistance profile ofthe training cell lines. A marker gene selection process was carried outby KNN algorithm which fed only the genes with higher correlation withthe target class. The KNN algorithm sets the class of the data point tothe majority class appearing in the k closest training set samples. Thismarker selection is done by sorting the genes according to thesignal-to-noise statistics, [μ1(g)−μ2(g)]/[σ1(g)+σ2(g)], described asthe correlation function where [μ1(g), μ2(g)] and [σ1(g), σ2(g)] denotethe means and SDs of the expression levels of gene g for the samples inclass 1 and class 2, respectively. The magnitude of correlation valuesindicates the strength of the correlation between gene expression andclass distinction.

Leave-One-Out Cross-Validation Analysis and Random Classification

Predictors with 1-250 genes were used for cross-validation of thetraining set. For each predictor, cross-validation was performed withthe entire training set; one cell line was removed, the classifier wastrained on the remaining cell lines and then tested for its ability toclassify the withheld cell line. This procedure was repeated for eachcell line in the training set. For random classification analysis,GeneCluster was used to generate random class vectors and calculateerror rates.

Clustering and Tree View

Gene expression data were analyzed by the software Cluster and TreeView.

Breast Tumors and Gene Expression Data

RNAs extracted from 175 breast tumors resected at the surgery wereobtained from the Karolinska Institute (Stockholm, Sweden). These RNAsamples were profiled using Affymetrix Human U133 sets and their geneexpression data were used for the analysis.

Results

Drug sensitivity data (IC₅₀) was used as a template for determining thephenotype of the cell lines as resistant or sensitive. Initially, twoseparate IC₅₀ data sets were generated for 23 breast cancer cell lines.As a first step for the analysis, the log(IC₅₀) value for each cell linewas calculated and normalized using the mean of log(IC₅₀)s and SD acrossthe cell lines (J. E. Staunton et al., P. N. A. S. USA. 98, 10787-10792(2001)) in each IC₅₀ data panel. Then the cell lines were divided intotwo classes using the following method; the normalized log(IC₅₀)s abovethe mean are defined as resistant and below as sensitive (FIG. 1). Aftercomparing the classification of the cell lines in the two data sets, 18cell lines that displayed the consistent classification and IC₅₀ valuesin two separate experiments were selected and utilized for markerselection.

Subsequently, the gene expression data of the 18 cell lines wereanalyzed to identify genes that were highly correlated with observedphenotype defined as sensitive or resistant. From the GeneClusteranalysis, classifiers that consisted of up to 250 correlated genes wereselected and tested through leave-one out cross validation; by holdingback one cell line, training on the remaining cell lines, predicting theclass of the withheld cell line, and repeating this cycle for each cellline in the training set. Each gene was ranked according to thecorrelation in the training set between its expression level and thesensitivity-resistance class distinction. Each classifier identifiedfrom the analysis was evaluated with the error rate as shown in the FIG.2. In order to assess whether or not the classifiers can be observed bychance, the error rates calculated from random classification wereexamined. Shown as an example in FIG. 3, error rates generated fromrandom classifications were significantly higher than that fromIC₅₀-based classification.

From the GeneCluster analysis, 200 genes (Tables 1 and 2) wereidentified whose expression levels were highly correlated with thesensitivity-resistance class distinction based on the KNN analysis andthe T-test. Among these genes, the 50 marker candidates most closelycorrelated with sensitivity-resistance class distinction (first 25sensitive markers of Table 1 and first 25 resistant markers of Table 2)were selected for further analysis.

As shown in FIG. 4, these 50 genes showed distinct expression patternsbetween sensitive and resistant cell lines. For example, the top 25markers correlated with sensitivity (one of which was Proteasomesubunit, beta type 8 (LMP7)) as shown in FIG. 4 were highly expressed(shown in red) in sensitive cell lines, but at a lower level (shown inblue) in the resistant cell lines. In contrast, the top 25 markerscorrelated with resistance showed the opposite expression pattern asthese genes were highly expressed in the resistant cell lines, but at alower level in the sensitive cell lines.

Among 200 genes identified, it is interesting to find estrogen receptor(ER) as one of the resistance markers. As shown in FIG. 4, ER expressionlevels were highly correlated with the resistance to ixabepilone. ER washighly expressed in the resistant cell lines, but its expression wasvery low in the sensitive cell lines. Although the resistance mechanismof ER is not obvious, the data suggests that ER might be involved indrug resistance associated with microtubule stabilizing agents. In fact,ER was also found as a resistance marker in our analysis of paclitaxel(data not shown). In addition to ER, a microtubule-associated protein,tau (Tau), was also identified as one of the resistance markers. Thisprotein has been proposed to bind close to the Taxol® binding site onβ-tubulin and stabilize microtubules in a similar way to Taxol® (S. Karet al., EMBO J., 22, 70-77. (2003)). Therefore, Tau is likely to affectthe Taxol® bound to microtubules and, presumably, ixabepilone in asimilar way since ixabepilone binds at the same site as paclitaxel onβ-tubulin. Interestingly, Tau is estrogen induced (M. West et al., P. N.A. S. USA, 98, 11462-11467 (2001)). Evidently, they seem to beco-regulated as shown in a plot of Tau expression level against ER (FIG.5). Their correlation coefficient value is 0.7.

Among the sensitivity markers identified, LMP7 is particularlyinteresting because it appears to be connected to Tau's function. Ingeneral, the proteasome is a multicatalytic proteinase complexresponsible for the degradation of most intracellular proteins,including proteins crucial to cell cycle regulation and programmed celldeath, or apoptosis (P. Voorhees et al., Clin. Cancer Res., 9, 6316-6325(2003)). Among many proteins processed by the proteasome, Tau isdegraded by the 20S proteasome in vitro in an ubiquitin-independentmanner (D. David et al., J. of Neurochemistry, 83, 176-185 (2002)). Thissupports LMP7 as one of the sensitivity markers because LMP7 presumablyfacilitates interaction between ixabepilone and microtubules bydegrading Tau and making ixabepilone more accessible to themicrotubules.

One type of drug resistance mechanism is based on the function of agroup of transporter proteins, able to prevent the intracellularaccumulation of anticancer drugs by an efflux mechanisms (F. Leonessa etal., Endocr. Relat. Cancer., 10, 43-73 (2003)). Several transportergenes were identified as potential resistance markers as they werehighly expressed in the resistant cell lines. These genes includeATP-binding cassette, sub-family G (WHITE), member 1 and ATP-bindingcassette, sub-family A (ABC1), member 3. They are ATP dependenttransporters which may be involved in lipid transport, and act as anefflux pump for chemotherapeutics drugs respectively (M. Gottesman etal., Nat. Rev. Cancer., January; 2(1):48-58 (2002)).

In addition, genes implied in microtubule functions are particularlyinteresting since ixabepilone is a microtubule-stabilizing agents.Microtubules are essential components of the cytoskeleton and involvedin cell motility and transport, and maintenance of cell shape. Thedynamic nature of a microtubule whose ability to polymerize anddepolymerize, is essential for the segregation of chromosomes duringmitosis (C. Bode et al., Biochemistry, 41, 3870-3874 (2002)). Therefore,marker genes such as midline 1 (C. Berti et al., BMC Cell Biol.,February 29; 5(1):9 (2004)) and annexin A1 (L. C. Alldridge et al., Exp.Cell Res., October 15; 290(1):93-107 (2003)) that are implied in thosefunctions can be involved in the mechanism of drug resistance. Thebiomarkers are categorized by their biological functions in Tables 1 and2.

To study the use of these genes as response prediction markers in vivo,the expression pattern of these 50 genes in 175 breast cancer biopsiesobtained from the Karolinska Institute was examined. The 50 genes wereused to cluster the expression patterns of tumors. As shown in FIG. 6,these tumors were found to show patterns of expression that allowedsub-classification of these tumors into distinct groups as seen in thecell line study. Among many genes, Tau and ER were examined in tumorswhich were identified as resistance markers from cell lines. As shown inthe FIG. 7, there is a trend in which Tau and ER seem to correlate asseen in the cell line study. In fact, both genes are highly expressed ina subset of tumors. These tumors are presumed to be non-responders forixabepilone treatment.

Example 2 Further Evaluation of ER and Tau Biomarkers

Estrogen receptor (ER) and tau (Tau) were identified as biomarkers sincetheir expression patterns were highly correlated with resistance toixabepilone. In addition, it was found that the ER pathway was the mostimplicated biological network for resistance to ixabepilone based on thepathway analysis using preclinical candidate markers (FIGS. 9 and 10).Interestingly, Tau was recently identified as the gene most correlatedwith pathological complete response for T/FAC neoadjuvant treatment inbreast cancer patients (M. Ayers et al, J. Clin. Oncol., 22(12):2284-93(2004); R. Rouzier et al., P.N.A.S., June 7; 102(23):8315-20 (2005)).Following this report, our preclinical study on paclitaxel supported theclinical findings of Tau as a novel mediator of paclitaxel sensitivity(P. Wagner et al., Cell Cycle, September; 4(9):1149-52 (2005)). ER andTau were evaluated for their predictability of response to ixabepilonein CA163-080 trial.

Methods CA163-080 Study

CA163-080 is an exploratory genomic phase II study that was conducted inbreast cancer patients who received ixabepilone as a neoadjuvanttreatment. The primary objective of this study was to identifypredictive markers of response to ixabepilone through gene expressionprofiling of pre-treatment breast cancer biopsies. Patients withinvasive stage IIA-IIIB breast adenocarcinoma (tumor size≧3 cm diameter)received 40 mg/m² ixabepilone as a 3-hour infusion on Day 1 for up tofour 21-day cycles, followed by surgery within 3-4 weeks of completionof chemotherapy. A total of 164 patients were enrolled in this study.Biopsies for gene expression analysis were obtained both pre- andpost-treatment. Upon isolation of biopsies from the patients, sampleswere either snap frozen in liquid nitrogen or placed into RNAlatersolution overnight, followed by removal from the RNAlater solution. Allsamples were kept at −70° C. until use.

Evaluation of Pathological Response

Pathological response was assessed using the Sataloff classificationsystem (D. Sataloff et al., J. Am. Coll. Surg., 180(3):297-306 (1995))and used as an end point for the pharmacogenomic analysis. Thepathologic response was evaluated in the primary tumor site at the endof treatment and prior to surgery by assessing histologic changescompared with baseline as following: At the primary tumor site, cellularmodifications were evaluated in both the infiltrating tumoral componentand in the possible ductal component, to determine viable residualinfiltrating component (% of total tumoral mass); residual ductalcomponent (% of total tumoral mass); the mitotic index. PathologicComplete Response (pCR) in the breast only was defined as T-A, Total ornear total therapeutic effect in primary site. Based on this criteria,responders included patients with pCR while non-responders includedpatients who failed to demonstrate pCR. The response rate was defined asthe number of responders divided by the number of treated patients.

Gene Expression Profiling

Total RNA was isolated using the RNeasy Mini kit (Qiagen) according tothe manufacturer's instructions by Karolinska Institute (Stockholm,Sweden). A total of 134 patients with more than 1 μg of total RNA withgood quality were included in the data set for the final genomicanalysis. Samples were profiled in a randomized order by batches tominimize the experimental bias. Each batch consisted of about 15 subjectsamples and 2 experimental controls using RNA extracted from HeLa cells.The expression profiling was done following a complete randomizationwith an effort to balance the number of samples from two tissuecollection procedures (RNAlater and liquid nitrogen), two mRNApreparation methods (standard and DNA supernatants), tissue collectionsites, and time of RNA sample preparation within in each batch. The mRNAsamples from each subject was processed with HG-U133A 2.0 GeneChip®arrays on the Affymetrix platform and quantitated with GeneChip®Operating Software (GCOS) V1.0 (Affymetrix). The HG-U133A 2.0 GeneChip®array consists of about 22,276 probe sets, each containing about 15perfect match and corresponding mismatch 25mer oligonucleotide probesfrom specific gene sequences.

Gene Expression Data Processing

The gene expression data were transformed using base two logarithm. TheRobust Multichip Average (RMA) method (C. Clopper et al., Biometrika,26:404-13 (1934)) was used to normalize the raw expression data. Thegene expression measures of each gene were centered at zero and rescaledto have a 1-unit standard deviation.

Stromal Effects in Tumor Biopsies

A hierarchical clustering analysis was performed in order to examinemolecular profiles of tumor biopsies (FIG. 10). Among the two highestlevel clusters, the tumor samples from three Russian sites (site numbers16, 24 and 25) were mostly clustered in the first cluster (Fisher'sexact test, p-value <0.01). It appeared that genes implied in lymphocytefunctions such as MHC, CD antigen, and IgG were enriched in thiscluster. Therefore, this led to the concern that the tumors from thethree Russian sites contained more stroma in the biopsies than othersites, thus contaminating the RNA samples with respect to geneexpression for tumor tissue alone. In addition, the mean tumor size fromthe three Russian sites (16, 24 and 25) was larger than that for theother sites (mean 5.43 vs. mean 4.55, t-test p-value=0.022). Moreover,the pCR response rate was lower than that of the other sites (pCR 19.8%v.s. 17.2%, chi-squared p-value=0.73). This suggested that tumors fromthe three Russian sites were distinct from the others. Thus, a subgroupanalysis excluding the three Russian sites was also performed.

Statistical Analysis

Logistic regression (F. Hsieh et al., Stat. Med., 17(14):1623-34 (1998))was used to explore the relationships between the expression of genesand response to ixabepilone. The following model was fitted for eachgene separately:

${\log ( \frac{\Pr ( {Y =  1 \middle| X } )}{1 - {\Pr ( {Y =  1 \middle| X } )}} )} = {b_{0} + {b_{1}X}}$

where Y=1 represents a responder and X is the gene expression measure.For each gene, the probability from a two-tailed Score test of whetherthe estimate of b₁=0 was used to rank the most interesting genes forfurther investigation. e^(b1) is the odds ratio of being a non-responderfor a one unit increase in gene expression relative to the averageexpression for the sample of subjects. Odds ratios and 95% confidencelimits were reported.

Subjects were randomly assigned to the equal sized training set (n=67)or the test set (n=67), for responders and non-responders groupsseparately. The gene expression of ER and Tau were considered aspotential predictors for response. Single logistic regression (SLR) wasused to build the predictive model based on the training set, and themodel performance was assessed on the test set. The prediction error,sensitivity, specificity, PPV (positive predictive value), and NPV(negative predictive value) as well as their 95% confidence intervals ofthe SLR model were estimated.

Results Estrogen Receptor (ER) and Tau

For ER, patients whose predicted probability of being responders wasgreater than 0.3 were classified as responders. The ER prognosticsensitivity, specificity, PPV, NPV, and their 95% confidence intervalsof the SLR model are 0.64 (0.35, 0.85), 0.79 (0.66, 0.87), 0.37 (0.19,0.59), and 0.92 (0.80, 0.97), respectively. For Tau, patients whosepredicted probability of being responders was greater than 0.25 wereclassified as responders. The Tau prognostic sensitivity, specificity,PPV, NPV, and their 95% confidence intervals of the SLR model are 0.55(0.28, 0.79), 0.73 (0.60, 0.83), 0.29 (0.14, 0.50), and 0.89 (0.77,0.95), respectively.

Estrogen Receptor (ER) and Tau without Russian Sites 16, 24 and 25

For ER and Tau separately as SLR predictors, patients whose predictedprobability of being responders was greater than 0.5 were classified asresponders. The estrogen receptor 1 prognostic sensitivity, specificity,PPV, NPV and their 95% confidence intervals of the SLR model are 0.67(0.35, 0.88), 0.83 (0.69, 0.92), 0.46 (0.23, 0.71), and 0.92 (0.79,0.97), respectively. The Tau prognostic sensitivity, specificity, PPV,NPV, and their 95% confidence intervals of the SLR model are 0.44 (0.19,0.73), 0.88 (0.75, 0.95), 0.44 (0.19, 0.73), and 0.88 (0.75, 0.95),respectively.

CONCLUSION/DISCUSSION

A total of 164 patients were enrolled in CA163-080 study. The qualityand quantity of RNA samples obtained from pre-treatment biopsies wasfairly good as 134 patients (85%) had RNA samples with >1 μg goodquality which did not require additional amplification for geneexpression profiling. Stromal contamination in the tumor biopsies wasraised as a potential problem for the analysis. It appeared that thethree Russian sites 16, 24 and 25 might have more stromal tissues in thesamples compared to others based on the hierarchical clusteringanalysis. In addition, the tumors from these three Russian sites werelarger than others at baseline. Although further analysis is needed toconfirm this hypothesis, it raised an important issue for analyzingclinical samples that are inherently heterogeneous.

Among preclinical candidate markers, ER and Tau were examined inCA163-080 for their predictability. In our preclinical work, ER and Tauhad been identified as biomarkers since their expression patterns werehighly correlated with resistance to ixabepilone. In CA163-080, ERpredicted well for pCR whether or not the three Russian sites wereincluded in the analysis. However, the highest PPV was obtained whenthese sites were excluded. In another study finding predictive markersof response to combination chemotherapy with paclitaxel, 5-Fluorouracil,adriamycin and cyclophosphamide, the ER regulated gene Tau wasidentified as the best predictor of response (M. Ayers et al., J. Clin.Oncol., 22(12):2284-93 (2004)). Work done by this group has alsodemonstrated in vitro that knocking down Tau levels using smallinterfering RNA (siRNA) increases the sensitivity of breast cancer celllines to paclitaxel treatment (R. Rouzier et al., P.N.A.S., June 7;102(23):8315-20 (2005)). The proposed mechanism is that high levels ofTau inhibit binding of paclitaxel to the taxane binding site onβ-tubulin. Tau gene expression was therefore also examined for abilityto predict response to ixabepilone. The PPV (0.44) with this gene wassimilar to that for ER (0.46) in the subset excluding the 3 Russiansites.

Thus, ER and Tau demonstrated their utility as a predictors for responseto ixabepilone and can be used as biomarkers for identifying the pCRresponders to ixabepilone.

Example 3 Production of Antibodies Against the Biomarkers

Antibodies against the biomarkers can be prepared by a variety ofmethods. For example, cells expressing a biomarker polypeptide can beadministered to an animal to induce the production of sera containingpolyclonal antibodies directed to the expressed polypeptides. In oneaspect, the biomarker protein is prepared and isolated or otherwisepurified to render it substantially free of natural contaminants, usingtechniques commonly practiced in the art. Such a preparation is thenintroduced into an animal in order to produce polyclonal antisera ofgreater specific activity for the expressed and isolated polypeptide.

In one aspect, the antibodies of the invention are monoclonal antibodies(or protein binding fragments thereof). Cells expressing the biomarkerpolypeptide can be cultured in any suitable tissue culture medium,however, it is preferable to culture cells in Earle's modified Eagle'smedium supplemented to contain 10% fetal bovine serum (inactivated atabout 56° C.), and supplemented to contain about 10 g/l nonessentialamino acids, about 1,00 U/ml penicillin, and about 100 μg/mlstreptomycin.

The splenocytes of immunized (and boosted) mice can be extracted andfused with a suitable myeloma cell line. Any suitable myeloma cell linecan be employed in accordance with the invention, however, it ispreferable to employ the parent myeloma cell line (SP2/0), availablefrom the ATCC (Manassas, Va.). After fusion, the resulting hybridomacells are selectively maintained in HAT medium, and then cloned bylimiting dilution as described by Wands et al. (1981, Gastroenterology,80:225-232). The hybridoma cells obtained through such a selection arethen assayed to identify those cell clones that secrete antibodiescapable of binding to the polypeptide immunogen, or a portion thereof.

Alternatively, additional antibodies capable of binding to the biomarkerpolypeptide can be produced in a two-step procedure using anti-idiotypicantibodies. Such a method makes use of the fact that antibodies arethemselves antigens and, therefore, it is possible to obtain an antibodythat binds to a second antibody. In accordance with this method, proteinspecific antibodies can be used to immunize an animal, preferably amouse. The splenocytes of such an immunized animal are then used toproduce hybridoma cells, and the hybridoma cells are screened toidentify clones that produce an antibody whose ability to bind to theprotein-specific antibody can be blocked by the polypeptide. Suchantibodies comprise anti-idiotypic antibodies to the protein-specificantibody and can be used to immunize an animal to induce the formationof further protein-specific antibodies.

Example 4 Immunofluorescence Assays

The following immunofluorescence protocol may be used, for example, toverify biomarker protein expression on cells or, for example, to checkfor the presence of one or more antibodies that bind biomarkersexpressed on the surface of cells. Briefly, Lab-Tek II chamber slidesare coated overnight at 4° C. with 10 micrograms/milliliter (μg/ml) ofbovine collagen Type II in DPBS containing calcium and magnesium(DPBS++). The slides are then washed twice with cold DPBS++ and seededwith 8000 CHO—CCR5 or CHO pC4 transfected cells in a total volume of 125g and incubated at 37° C. in the presence of 95% oxygen/5% carbondioxide.

The culture medium is gently removed by aspiration and the adherentcells are washed twice with DPBS++ at ambient temperature. The slidesare blocked with DPBS++ containing 0.2% BSA (blocker) at 0-4° C. for onehour. The blocking solution is gently removed by aspiration, and 125 μlof antibody containing solution (an antibody containing solution may be,for example, a hybridoma culture supernatant which is usually usedundiluted, or serum/plasma which is usually diluted, e.g., a dilution ofabout 1/100 dilution). The slides are incubated for 1 hour at 0-4° C.Antibody solutions are then gently removed by aspiration and the cellsare washed five times with 400 μl of ice cold blocking solution. Next,125 μl of 1 μg/ml rhodamine labeled secondary antibody (e.g., anti-humanIgG) in blocker solution is added to the cells. Again, cells areincubated for 1 hour at 0-4° C.

The secondary antibody solution is then gently removed by aspiration andthe cells are washed three times with 400 μl of ice cold blockingsolution, and five times with cold DPBS++. The cells are then fixed with125 μl of 3.7% formaldehyde in DPBS++ for 15 minutes at ambienttemperature. Thereafter, the cells are washed five times with 400 μl ofDPBS++ at ambient temperature. Finally, the cells are mounted in 50%aqueous glycerol and viewed in a fluorescence microscope using rhodaminefilters.

Although the invention has been described in some detail by way ofillustration and example for purposes of clarity and understanding, itwill be apparent that certain changes and modifications may be practicedwithin the scope of the appended claims.

1. A method for predicting a resistance to a method of treating cancerof a mammal in need thereof comprising administering amicrotubule-stabilizing agent comprising ixabepilone, wherein the methodcomprises: (a) exposing said mammal to said agent; (b) following theexposing of step (a), measuring in a breast cancer tissue biologicalsample from the mammal the level of a biomarker comprising estrogenreceptor 1, wherein an increase in the level of the biomarker predicts aresistance to said method of treating cancer.
 2. The method of claim 1wherein said estrogen receptor 1 comprises a nucleotide sequenceencoding the amino acid sequence of SEQ ID NO:318.
 3. The method ofclaim 1 wherein said estrogen receptor 1 comprises the nucleotidesequence of SEQ ID NO:120.
 4. The method of claim 1 wherein saidestrogen receptor 1 comprises the amino acid sequence of SEQ ID NO:318.5. The method of claim 1 where said measuring comprises using the RobustMultichip Average (RMA) method to normalize expression data.